Well the refugees must be angry about something. They wouldn't have gone up in arms if they were being treated fairly. They do the work, but they are the ones that have to put up with poor living conditions, disease, and rationing. Do you think the Founders have to do that? The Resistance put everything on the line when they go into war. If they win, then there'll be fair distribution for all until everything can be sustained (or that's what I thought the plan was. Apparently, the goal is to "escape the Ark. Why the Founders and Security don't let them leave is something we'll have to find out from playing) If they lose, then they risk punishment for all the refugees. Work will be longer and harder, and rations will be less, and inequality will continue.
If they leave now everything will go to [censored], becuase now they have made it be able to work somewhat for the 50.000 people that are there, if the majority of the workers leave, the Ark is lost, and if their mission to find land is a failure, then whoop-ass mankind just got extinct
And it is unknown wether the Founders actually are stocking up on water, but really, I think not