My usual response to these kinds of posts is Rivals + Auto-fire weapons + low crit. Or gas grenades. Or snipers. those are still a viable options here, but lets look at some less heavy-handed options.
Is there any reason the pirates aren't already alerted to their presence, or could be at a moment's notice? That seems like the easiest way. Nothing like a modified probe droid to find them...
Anyway, I would balk at the idea that one guy could subdue an entire crew, it's possible the player has an inflated idea of how much his character can take on, and doesn't know how far he can expect to get, so you might want to point out the difficulties. The entrance is only going to get him to the base level, and each section has it's own set of doors that can be closed. The bridge is probably closed by default, it's a Sil5 Gozanti after all.
Also, the crew knows the ship, where all the buttons are, how to lock sections off, etc. His vibrorapier isn't going to cut through the blast doors, and that will give the crew time to call for help. If they fight hand to hand, defending a doorway provides cover (one setback), and I'd argue hard cover (2 setback) because of the knowledge of the ship.
But if you want to dissuade him from even making the attempt, only a show of power that the player can respect in-game is going to deter him.
I think what whafrog has proposed is your best bet. Make his plan a total PITA. Lots of crew, tight spaces, blind corners, ambushes, pirates in groups, locked doors, etc. Give him plenty of opportunity to see that it's not going the be easy, there will likely be fatalities, and he probably still won't succeed.
If he persists, raise the alarm. Make it clear that the rest of his party taking tons of fire is his fault. At that point he can persist in trying to steal the ship, leaving his employers to die (and then he won't get paid), or he can go help them, outside the ship, at which point you lock it off and the game proceeds as normal.
Also point out to the player what you explained to us: There's no reason for the party to come get him afterwards. If the character is on this mission for money, then he should have no problem roleplaying that, which means he should stay close to make sure he gets paid and not abandoned. Remind him of the risk, too: If he gets caught, what incentive does the party have to come to his aid?
Alternatively, make it clear that the pirates are waaaaaay more scared of the BBEG than they are of his pointy stick. They will fight to the death to defend their ship, which is basically their livelihood. So they'll keep coming at him, he'll have to keep killing them, and he'll have to gobs of conflict. They came for the crates, not for the ship. To accomplish their goals, he doesn't need to be on the ship, he doesn't need to steal the ship, so there's no justifiable reason for him to be killing pirates to achieve either goal.
The point is, the player is trying to outsmart the plot. Not necessarily on purpose, but it's still effectively what he's trying to do.
Don't let him.
You can reward him for being creative by slowing down the ship or making it less capable, but don't let him completely remove the ship from play (If destroys the engine, repair it while they're loading the crates on their own ship; If he steals a part, they have a spare; if we wipes the memory core, they restore from a back up, etc, etc). He's leveraging his character's stats and his roleplaying ability to make things hard for you, and it's okay for you to leverage everything at your disposal (Basically the rest of the universe) to make it equally hard for him. Give him plenty of warning to back down from that course, but if he persists, throw the consequences of his actions at him. HARD. It'll make him think twice about going gung-ho after getting warned away from a course of action.