Personally, I would say that after 15-20 minutes onboard an enemy vessel, they will be cut off from portions of the ship by sealed bulkheads and they will be running into larger and better coordinated defences (20 to 30 armsmen at every junction with at least 2 crewed support weapons in each group - shotcannon, heavy stubber etc). I would rule that any hit-AND-RUN attackers who were not back on their own ship by the end of the 30 mins would be killed or captured (if they burned a fate point)...
Two things to remember:
1. They teleported over with ordinance (melta or krak charges most likley) to carry out their sabotage; after 1 strategic turn, they are down to their personal arms
2. Void suits don't protect diddly if they're full of holes, which they should be after 20 minutes on a hostile craft...
If your players insist that they could handle it, I'd play it out... stress the huge numbers of armsmen and ratings they can see converging on them at every corridor (use the Horde rules from DW if you have them to speed the combat along). As a rule of thumb, I assume 10% of a ships crew population are trained armsmen, so even for a raider class ship, you're looking at about 2,000 troops before the ships command crew even show up. If they do persist with the idea and you play it out, please let us know how it goes.
Best of luck