I would have to assume so. There was the infamous break in S3 where she left in the middle of a major storyline that couldn't have gone down well. But the stuff listed in the book seems trite when it was a problem for others. Nic himself says he was very unreliable and they fought to keep him around. There must have been more going on or the problems with lines/marks were very, very serious.

I really don't think she was fired for the pregnancy. From what I read, S4 of Angel was supposed to mirror Becoming, with Angel/Cordy fighting and him killing her. Which is to say she was done after S4 from the get-go.