This same thing happened to me and basically made it impossible to continue. Even if I had no over-colonization unhappiness I couldn't stack enough happiness to overcome the malus. Then, even after my non-craver pops (a pretty insignificant portion of my empire) were gone the malus remained. The election system is really unclear as well. Shouldn't non-craver pops be enslaved and not get a vote?

On the flip side I took over a bunch of craver planets in a Lumeris game and the couldn't get rid of the craver pops that would eventually make my planets worthless. It's like the game thinks I have population control options but I don't as far as I can tell. If i had been able to purge the problem pops in either game I don't think this would have been and issue. 

I don't think that influencing the elections has any effect other than a slight boost to your preferred party's numbers.

If you hover the mouse over the happiness counter what does it say?