I was thinking two things about the FTL Engine Room scene: One) The FTL drive looked like something out of Galaxy Quest. Those spinning reciprocating sleeves would be impossible without CGI. Two) The marks that the Chief is looking at look to me like claw gouges more than cracks. Maybe there's still a Centurion or two from that one raid from Season 1 (or was it 2?) Or some kind of space beastie?
But I do agree that if Galactica had jumped, it might have been too much for that structure, possibly causing the loss of the flagship and all hands on board. That might also mean that for better or worse, Galactica is stuck in the system until repairs can be made.
However, that whole sequence brings up one glaring problem: What kind of engine room is it that no one ever visits? Watching the show Friday night, I got the impression that the FTL drive room is off-limits to personnel (no technicians; no guards; crappy lighting; and large, fast-moving machinery without safety guards). If that's the case, it's no wonder that the damage to the bulkhead wouldn't be noticed. But, is that any way to design a star ship?