Cristos was the replacement LaFortier's followers wanted. He wasn't the natural next Senior Council member. The natural replacement was Klaus the Toymaker. Everyone senior to him had already passed and/or been absent at least twice, and maybe even killed. The only way Cristos was able to skip to the front of the line was by threatening to destroy the Council.
If Cristos was Black Council, he would have feigned acceptance of Klaus on the part of his constituency and then told his constituency that they had been railroaded by the Merlin.
That's the best reasoning I can come up with for "Cristos isn't Black Council," and it relies on the assumption that Cristos couldn't put himself forward in the election process once Klaus accepted the nomination, which isn't an assumption I'm willing to make.
There's obviously more than one bad guy in the Council. Cristos is a good bet. If I had to pick someone as the bad guy on the Council, I don't see a better pick. Long story short, I agree with you, but I just like the idea that Cristos is some stupid puppet. Kind of how I like the idea of winning the lottery but don't think I'm going to win (except I have better, if not good, odds with Cristos).
On a side note, we've been spelling Cristos wrong.