Dude, you're talking about a group of people that have the tactical ability of a chimpanzee. Do you really think that Command would ever scan the ship for lifesigns before entering? Command obviously never learned from its mistakes from the previous war with the shivans, and got careless with the constant flaunting of the "superior technolgy". Then the shivans sent in 80 juggernauts and blew up Capella killing who know how many millions of people in a giant supernova.
At any rate, the shivans are xenophobes. They're not going to sit idly by while we infest one of their capital ships. They'll fight to the bitter end to keep us out. That disaster of a battle only took place on a Cain-class cruiser. What do you think would happen if we got ourselves a Demon let alone a Ravana or Sathanas? The GTVA could have another Lucifer on their hands (or more than one!) and given what it took to stop the last one, I don't think they'd have much of a chance in hell of winning.