So much drama could have been avoided if Elita and her crew had just spoken plainly. "This is an evil Titan we've got under lock and key. Waking him will do more harm than good."
Not out of the realm of possibility. Also a good point, though they acknowledge in story its pretty much a last desperate gamble to keep the Undead Titans from killing everyone.
That's true, but they failed to think about the reasons Elita could have for not awaking the Titan or the aftermath of their plan; like what if hijacking the Titian starts a war?
The "crew" Elita included were prisoners, and all the spare parts were the former crew and guards is the big secret I'm guessing.