It's a battle you can win with forking and shunning any plugins they take over. That will show developers that injecting Kite into your popular project leads to it becoming very unpopular, very quickly.
Is there a reliable way to search github for projects that are managed by Kite? Looks like it is only mentioned in the readme, and it would be simple for kite to simply not put in references to kite.
Probably, but it could be an on-going fight as server names or even library names could change over time. I guess in the long run it will become like any other virus/malware scanning.
That's not a battle you can win with manual diligence.