Spoiler!!!!!!! Guess we know why there was a Nexus Uprising.

Pretty much. If I had to guess it is probably a combination of lack of response to failing colonies and cries for help in the face of Khett attacks falling on deaf ears for over a year which have caused the Nexus uprising. 

That or potentially shutting down or threatening to shutdown the life support of non essential staff to keep the Nexus going might do it.

Not really, it's not like the A.I.-Leadership is any better of than them (they are all on the Nexus, so attacks threaten them ALL!)...I hope we can stamp out those traitors (when people are in danger - especially if it's live threatening - then you don't rebell because your former enemies (they people you complain about or who you are complaining to suddenly are - or at least should be - your best friends (the enemy of my enemy is my friend!) are your friends now and you should fight alongside them! If you don't, then you are guilty of treason IMHO (especially if you steal important supplies, ships, technology, weapons etc. and run off!) and that makes you a dead man walking (summary execution is a fitting end for traitors IMHO!))

If they had waited till the situation had run its course and started complaining then?

I'd be the FIRST to fucking listen and I'd help negotiate a compromise (or I'd fully support the rebells if possible and if the A.I.-Leadership doesn't agree to a compromise!), but this is not the way!

greetings LAX