You see Kuvira's original intentions were completely right at the beginning. The Avatar was out of commission and the Earth Kingdom was in complete disarray. She took it upon herself to rebuild and to get rid of the anarchy that had settled in the Kingdom. She accomplished that. She wanted to build a people-centric economically prosperous empire instead of a corrupt monarchy.
It was only when she used the Earth Empire's military might to threaten the other nations that she really crossed the line IMO. And even though, look at what Rhiko did. The President wanted to use a puppet monarch to pull the strings behind the scenes and be in single control of the largest economic and population power in the world.
So really, Korra was pretty much stuck between two bad guys that season. It was awesome.