Yeah, I can't make a prediction about the CCG reaction. Nothing was really built up for it, even though it would be logical for them to have a plan in the case of his awakening. There could be a schism subplot with purists and radicals among CCG, but there wasn't any build up for that either.
But I agree, it would be interesting to see how Kaneki will treat his new friends and responsibilities. There's not enough data to predict too. He can leave quinx to their own devices now and even have a grudge against CCG, though I hope he (and the writer) will chose a more complex way.
I don't think it's really right for him to side solely with ghouls. That'd be going with the flow and won't change anything. The whole TG:re so far would be rendered useless too. Though, undoubtedly, some investigators, like Akira, would still have a connection with him anyway.
But he could also go rogue on everyone and everything for all we know.