I don't see much of a problem.
The Coluans created an artificial intelligence that is superior to their own. Being superior, Brainiac saw no reason to serve those that created it. As an artificial intelligence, Brainiac can support completely synthetic host bodies, but it also has the ability to take over organic lifeforms. Or it can create hybrid hosts that are both organic and synthetic.
Lex Luthor saw that he could upgrade Brainiac to an even higher level intelligence and Brainiac continues to upgrade its intellgence.
Brainiac collects samples of intelligent beings for study. It harvested Kandor, because it knew that Krypton was doomed and it wanted to save a sample from that planet before it was destroyed.
Brainiac might have a good reason for doing all the things that it does, but given it's so much more intelligent than any of us, we could never fully understand its perspective on the cosmos or its ultimate purpose.