What you have here is a meta-game issue, sometimes known as the "I'm not going in that scary scary dungeon!" problem. Obviously, the Commodore needs the PCs for some reason, and she has good reason to believe that they won't comply with her wishes just because she bats her eyes and says 'pretty please". She had to have some sort of plan for getting them to cooperate with her when they weren't immediately under her thumb, which argues for either a strong positive motivator ("I'll make sure your goal of X is met", and X may be money, or fame, or something else the PCs want), a strong negative motivator ("I'll make your lives so awful that you'll wish you'd never been born"), or some combination thereof. As the GM, it's your job to have figured this out beforehand; module creators can sometimes give you a few ideas, but they won't know anything about your group or how it works. Also, while some adventures tell interesting stories, others are not exactly models of consistency with other material, and that can pose a problem sometimes.
In this situation, there has to be a reason that the Commodore doesn't just say, "I'm taking your ship away, have a nice life!" (besides the obvious "there's no adventure if that happens"). She needs the PCs for some reason, and unless she's planning on sending along her own flunkies to ensure PC compliance with her directives (in which case, why does she need the PCs?), she shouldn't do anything to strain relations with them. Taking their ship into naval service is unlikely to sit well with them, so she's got to do something to keep them from just running for the border as soon as they're clear. If they're in money trouble, she could make it go away; if they have legal issues, she might be able to arrange a pardon. This is the time at which she needs to reveal her plan to the PCs, and you can play it several different ways.
The "space-lawyer" ex-pirate can be threatened with whatever punishment you think the player will put up with without quitting the game. It might be as blatant as "The guards put you into the general prison population without removing your manacles and say, 'Go get him guys! He's yours for the night!' while banjo music plays in the background," or it might be as subtle as leaving him in solitary confinement until his friends come for him, having been convinced to work for the Commodore. This will depend on just how brutal you feel like portraying Imperial officials; people have differing opinions on the subject. I'd probably settle for a middle ground, threatening to expose him for crimes committed during his pirate career that have an unpleasant local penalty, and point out that there will be evidence aplenty to convict him, even if Naval Intelligence has to manufacture it.
For the other players, the Commodore can stay with her earlier plan, whatever that may be. She can also use the fate of their mouthy friend as an extra hold over them, if she thinks they will care about what happens to him.
Her ultimate goal should be carefully chosen. You can't just file the serial numbers off a WWII movie; there are complications that vary with the setting. For example, if the PCs might encounter resistance, she'll need to think about the idea that they will be interrogated by someone with Truth Drug or telepathy; if the PCs know anything, it's possible that the enemy might discover it. This does pose possibilities if she's setting them up to take a fall, but that's getting pretty baroque.