I suppose a non-stutterwarp force could just stay close to the atmosphere (up to about 12,000 km for Earth) and watch as the cool stutterwarp missiles sputter as they approach, or mix it up with the warpships as they drop to reasonable speeds and weapon range. Granted, the FTL guys could set up a blockade but they really wouldnt dare engage, completely losing thier advantage to the conventional ships in the gravity zone.
I personally find your view of the situation more interesting because it introduces more nuance and variation to the universe. Unfortunately it isn't borne out by the combat rules themselves. GDW for whatever reason was absolutely enamored with having space combat occur at huge distances. It happens in Traveller. 2300 has it as well.
Remember, a 2300 space hex is 600,000km across. Starship lasers in 2300 are listed as shooting at a range of two hexes. So they're able to do damage at ranges of 1,200,000km at the very least.
(Side note: Unfortunately I'm not up on my Physics but doesn't that range seem a bit ... extreme? Taking into account the Inverse-Square Law and how much megawattage 2300 lasers are rated at, it seems unrealistic. I sometimes suspect that GDW's writers didn't really know about the Inverse-Square law and only thought about the lack of atmospheric attenuation when determining space combat ranges.)
As Whartung points out, 2300's sensors and gunnery computers are designed to hit something moving effectively faster than lightspeed. Due to the nature of Stutterwarp in regards to inertia (it doesn't really have any) and how Stutterwarps probably flicker in a somehow random pattern to make it harder to hit, essentially all weapons in 2300 have a very high rate of fire and use prediction software to simply shoot a whole bunch of shots into the general area where you think the ship will be when your lightspeed beams reach there and hope a few hit.
0.1g Gravity gradients and serious degradation of performance occurs relatively close-in to planets (a lot less than 1.2 million km iirc). In other words, the range of weapons in 2300 are a b*tch for people lower down (in the higher gravity range). They don't have to come down to where their own efficiency takes huge hits. Ships further up can shoot you to pieces from range where they still have pretty good efficiency. They can lob detonation lasers as well. It's essentially impossible for conventional spaceships to evade any of it. Only the mad flickering about of Stutterwarp allows evading hits.
But it gets worse.
The lasers of 2300 become much more effective as they no longer have to sweep fire into an area to hope to hit. Instead they concentrate on a single effectively stationary point. Assuming they still have to fire pulses due to the nature of their optics and power supplies, that 1x1+1 laser still will become something like a 1x20 monster. A 2x14 detonation laser might become some 2x40 vorpal weapon. In neither case do the lasers have to roll to hit anymore so all the shots are hitting.
How would you guys handle such an engagement? Use something like the vehicle rules? Just wing it?
If you're using 2300's combat system, I'd start using the vehicle rules and go with the idea that if you're playing an RPG you probably want to bias yourself heavily in favor of excitement and players making a difference instead of determinism, because determinism is what is going to happen if you go with straight 2300 rules distilled for near-orbit as demonstrated above.
Personally, I want to see things more dramatic, involving more rolling of dice by my players even at the sacrifice of some realism. In my 2300 universe, I made electronic warfare (EW) my excuse for this. An unarmed and unequipped freighter is going to be so much target practice for a freighter. However, a freighter equipped with a few guns and decent EW suite can make things more interesting. EW is of course is considered a weapon by naval authorities, but given the Kafer War, a lot of civilian ships in my universe carry EW suites. As a weapon, EW suites occupy a nebulous status where they're far less threatening than a detonation laser (which is still a nuclear weapon and a huge no-no for civilian ships in a lot cases), technically EW is non-lethal unlike a weaponized laser or particle accelerator, but despite all that, it's not entirely "defensive" and can still be used offensively to cause a lot of potentially deadly mischief.
As a result, most navies will wink and nod and look the other way at EW installations on civilian vessels. If you use an EW system in an inhabited system, expect to be detained by the authorities regardless of if you had a good reason or not - the court will determine if you had good reason. If it was obviously for good reason (like being chased by a Kafer ship that can be corroborated by Naval witnesses) they'll ask for your sensor records and an after-action report and send you on your way after maybe a day or two while they get the paperwork straightened out. If you didn't have a good reason, be ready for some serious legal trouble, starting with fines but might end at seizure of the ship and a prison sentence.
EW essentially shortens ranges because it jams accurate sensor returns. It includes omni-directional equipment as well as targeted transmission equipment. It can do things dazzle optics using lasers (which can be lower powered and longer ranged because it's trying to degrade the performance of telescopes by dazzling them, instead destroying them), jam radar, and so on. To be fully effective, EW requires a "gunner" to operate it. If a ship is attacked by an effective EW attack, it's effective combat range drops hugely. Of course, the closer you get to the EW target, the more effective the EW gets. Stutterwarp ships in gravity gradients sufficient for space combat still jump around a lot, so a good EW suite can allow you to evade that Kafer privateer long enough to get near enough to a planet where Naval forces can chase the Kafer ship away, or allow you land and hide amongst the ground clutter in uninhabited systems (that the Kafers might land too and send out search parties to look for the players is perfect, because now it's a nice easily handled player-scale combat where all the players can contribute).
Ships have countermeasures against EW of course, including things like burn-through for RADAR, or getting into a range where your weaponized lasers to destroy the EW suite's dazzle laser (targeting with this level of precision requires coming into near visual range), Radiation Homing Missiles and so on. Of course, in turn, Radiation Homing Missiles can be shot down by your own weaponized lasers set to point-defense, dazzle lasers can turned off and hidden under armored covers, and so on.
This all increases the number of rolls, options for action by the players to do things, which reduces the amount of determinism ... which was my goal in the first place.