As a test, I just tried building medical buildings to keep my Harpies happy. It took 25 medical buildings to barely make the Harpies happiness go over 0. Those 25 medical buildings in turn required 2 power buildings (it would be 4 if they weren’t Harpies). That cost a total of:
So if the medical buildings aren’t adjusted, then either we have to dedicate the first 83,000 of the native population solely to just keeping them happy (my 13km planet only has a max of 81k native pop) or we need to eliminate all native populations as quickly as possible in order to avoid the riots and costs. That math seems to give a firm answer in my mind, since a negative ROI doesn’t need much thought. Do we really want to tell our players that the best thing you can do with any native population is to kill them off as quickly as possible?
Therefore I suggest that we either reduce the requirements of the medical building, or increase the happiness gained from them, or both. I personally would reduce the population requirement to 1,000, increase the happiness gain to 0.3, and decrease the power requirement to 10 MW. This should make them profitable to leave alive even on smaller planets.