Homura shot Kyubey to keep Madoka from contracting. She was chill enough with coobs to hang out with him and let him ride around on her post-Madokami. She told him a story that was backed up by nothing about a girl who never existed retroactively, and coobie sealed her soul gem as a trap so that he could conduct experiments on Madoka to make energy collection more efficient.
Yes, you're not taking Rebellion as evidence. But the fact remains that the incubators pre- and post-Madokami did not change one bit. They still seek energy to prevent entropy, they still contract little girls to fight horrible monsters. The monsters changed, the system did not. The end result of the system, the witch consequence for the meguca and everything after that, was taken by Madoka's wish, but that's all. Even using just the series as evidence.
TL;DR: Coobie a shit, avoid if possible, deal with sparingly and great care if not. He is on his own side.