Re: Angel ep 100. Probably worth reading the wiki for it. Considering the initial episode plan, which was knocked on the head due to SMG being unavailable, it wouldn't surprise me about saying one thing to CC and the script being different. But, at the same time, I would think that that script change was due to the different direction they wanted to go in. Considering David Fury is also listed as writer, I don't think Whedon can be blamed for it. Or at least, blamed in the sense of "I'm going to be a dick to this actress". More likely he just realised it wrapped-up the character nicely, and helped move the story along for the final arc.
By all means, if someone wants to show me the source where someone says they did it for other reasons, I'm good with that. But *shrugs*
It's always going to be conjecture, but given how they treated Charisma in S4 there's a pattern of shiftiness there. Course, Fury openly criticised Lost after he left so he's not the sort to stay quiet about shitty behind the scenes stuff...