regards to "Magnus's observations are spot on" - I'd have to disagree depending on what you're referring to. ..."
I don't want to offend: poking holes too vigorously in someone's interesting ideas can sometimes be felt as an attack. And, I don't want to take the thread off on a tangent by debating a single plan over several posts. However, to be fair to both you and Magnus, I'll note some of my concerns. If you don't agree, I respect that and we'll move on from there - no divine law says my viewpoints are always right.
Your specific plan in this case involves a simulated biological emergency. Basic idea of spooking the captain is sound - a good grift involves getting your target to think with his desires or his fears rather than with his rational mind. Some concerns about the details because whether the details work is universe-dependent: some gamemasters or even some players might not have circumstances that let you contaminate the engineer's food unless you find some way to suborn the steward as well as the cargomaster. On a Subsidized Merchant, for example, the layout makes it easy for most of the crew to eat apart from the passengers; the passengers'll see the steward and medic regularly, see the engineer as he passes through from front to back, may only see the captain/pilot if he deigns to leave the forward area and visit with them. What is a cargomaster, by the way? I thought it was a dockside position, but you're describing it as a crew position.
Anyway, some universes or player groups may likewise have a medic and/or medical equipment competent to recognize the biological you're using - for many of them, a good microscope and a good medical database in the computer is all you need. If the medic recognizes it, the game is up: he'll know exactly what the risks are and aren't, and you can't spook the captain with a faux plague when he's getting competent guidance from his medic. You either have to suborn or disable the medic, or gamble on a true plague with all the risks that entails. At the point where you're suborning two crew - or three, if you count the cargomaster - you already control a fair portion of the crew of the typical small freighter and a complex grift is pointless; just suborn the engineer and take the ship in flight the old-fashioned way.
But, for the purpose of this discussion, we'll stipulate that there is an organism that simulates a more virulent disease and that cannot be identified with the resources available to a ship in flight (and, by extension, that the more virulent disease likewise cannot be identified except by symptoms with the resources aboard the ship). And, we'll stipulate that by some stratagem you've managed to infect the engineer and captain (the latter being easiest since he might have a practice of taking meals with the passengers, not uncommon on passenger ships).
Step 11 runs into problems. Unless you have suborned the medic, you have no control over who goes into cold sleep for medical reasons: only the medic and the captain have that authority. You also have no control over the captain: if he takes ill, he can devolve command to the navigator, pop some passenger out of cold sleep for a free ride, and take the berth himself. Might be some liability issues involved in waking a person into an epidemic situation but, if the guy wants to live bad enough, he'll deal with the fallout later. Or, the ship could have enough unoccupied berths to serve the need - we don't always fill all our beds on these trips. In my TU, giving Fast drug to someone with an active infection could be potentially fatal - there's no assurance that the pathogen will respond to the fast drug the same way your body does, and the medic knows that. But, that's quibbling: point is, you've managed to infect captain and engineer, taking them out of the opposing lineup, and whether they're in cold sleep or under fast drug or delirious in their quarters is just a technicality.
Step 12 is seriously problematic: there are very few pathogens that are both food-borne and contact-borne
1, fewer still that will present the same symptoms regardless of the means of transmission. By stipulating a faux pathogen that can be fed to others and can also transmit through the skin (your presumed method of making the vacc suits infectious), AND stipulating that it creates symptoms like a plague disease they'll recognize but not be able to diagnose with shipboard equipment, you will be seriously stretching the credulity of any player who has much knowledge of medicine - and Traveller players are remarkably well-informed on a wide variety of subjects. It begins to look like the faux organism is a man-made, very carefully tailored organism to be able to achieve all of those requirements, and tailoring an organism, while not impossible, suggests a much higher level of criminal sophistication than your standard grift would imply. Moreover, it's the kind of sophistication likely to attract serious official attention, so it's not something an organized crime group is likely to engage in unless the whole system is so seriously corrupted that they can do such things with relative impunity.
1(Airborne presents the same problems as contact-borne with the added caveat that it's hard to keep an airborne organism in the air in a very still enclosed environment like an unused vacc suit; it'd settle to surfaces. But, that again is quibbling; key point is a multivector organism that presents the same symptoms regardless of vector AND mimics a virulent organism is a stretch that will be difficult to sell to the players across from you.)
A second problem with Step 12 is it's very universe-dependent: it rests on assuming the navigators in that universe would respond as you describe them responding. In Magnus' universe, the navigator activates a biohazard routine that locks down the ship and warns everyone around that it's a plague ship. In my universe, the navigator locks himself in the bridge, locks down the maneuver drive and sets auto-routines in the computer against the possibility he might come down with and be incapacitated by the illness anyway - said autoroutines instructing the computer to broadcast a ship-in-distress/biohazard upon emergence from jumpspace along with enough details to help rescuers figure out what to do. Someone else might do something else entirely. Point is, there's no reasonable assurance the scenario ends with Anti-hijack off unless your particular universe operates that way; my scenario for example, has anti-hijack on with half of a code being broadcast with the distress signal - legitimate authorities would have the other half and be able to signal the ship to allow them on board.
(There's this neat trick my company uses: a numerical code that changes every minute, in a little digital key with a display that you carry, with the computer you want to access generating the same code on the same schedule using the same algorithm. If you don't have the key, you don't know the right code for that moment. Hacking involves getting your hands on the algorithm AND getting it timed to the algorithm in the target computer; easier is to bribe the programmer to program in a back door.)
Step 13 is one of those circular situations: to access the computer core, you need the passcodes; to get the passcodes, you need administrative access to the computer, or to some person willing to divulge them. Computer core is not accessible from passenger spaces - even a decentralized system will keep key components where only authorized personnel can get at them. Without that, there's no changing out memory cores short of cutting your way through a bulkhead - and if you can get those passcodes, then you likely can get the other codes you need to control the computer.
None of these are impossible problems. It's just that there might be more elegant solutions: for example, contriving to get a steward hired aboard who is actually a skilled hacker with knowledge of an exploit specific to that model of computer that, say, gives him access to environmental controls that allow him to adjust the atmosphere to quietly knock out the crew in the bridge and engineering space with hypoxia - or knock everyone out if he can't manage fine control. Then it's just a matter of him and his confederates in their O2 masks overpowering the medic, cutting their way into those spaces, tossing the corpses into one of the crew staterooms and pulling the computer switch you discussed - preferably before they hit jump, 'cause that's the ideal time to throw any possible pursuit by jumping someplace other than where the ship was intended to go. Or, have your little cuckoo-nestling steward feed a sedative to the crew in their meal and launch the takeover that way. Or arrange with your dockworker confederates to load a cargo with a hidden explosive beneath the bridge - assuming the layout of the ship permits such things and you can manage to suborn customs enough to engineer such an operation - and have it go off as the ship is outbound before jump, with a confederate ship bearing one of those jump-nets Aramis mentioned standing by to sweep up the damaged ship and be in jump space before the engineering crew can get their wits about them.
That last screws heck out of cargo value but the ship might be repaired and sold, or passengers ransomed, or crew and passengers dropped off someplace and ship stripped for the value of its drives and power plant. I wouldn't pull that on players who owned their own ship, nor is it feasible unless you're close to the border where you can take the ship someplace sophisticated enough to milk its value without The Man showing up to spoil your profit, but it might be a foil to set shipless players down someplace where they (and their fellow passengers) need to survive by their wits.