Here's an idea I've come up with recently. You've got crew insurrection, rebelions, ppp, boarding parties and the aligence subverter. How about if they weren't permanant, that they only Lasted 2 or 3 or at most 10-15 turns.
This could simulate a situation that seems to come up often TV sci-fi shows -- when the guy in charge defys the desk people to take a stand, point out an injustice and, once the point is made, start following orders again in time for next weeks episode, without any penalty.
Ok, thats a little dumb when that happens, we wouldn't like that happening in real life. But it would be a way to balance these effects.