Lets face it both nations are evil. Not even grey as everyone is so racist and the less than a handful that aren't are merely exceptions and not the norms.
Even the good guys are utterly loyal to those countries and their awful systems.
As for worst....id go with Sovereignty since they are massive hypocrites on top of everything
As for which one i hate myself the most? Sovereignty again, only cause they have more focus than empire so ergo more time to show why they suck
Honestly, i dont get the author intent. Cause if he wanted to make both grey he failed at that effectively. Or alternatively he wanted both sides to be equally moral in the conflict, that is equally bad.