The 'official' theory was that Joss and the other writers said that they just ran out of things for the character to do, and they couldn't think of anymore storylines for her. But Charisma did not want to leave, despite her new born son. (God, I can't believe Donovan will be 11 this year!)
But what [MENTION=9799]Taake[/MENTION] said is what has trickles down through fandom over the years. Charisma keeping quiet about her pregnancy until she physically couldn't anymore caused a lot of hasty rewrites in S4, which caused the choppy, disjointed and rushed feeling to the season, and Joss and the other writers weren't happy with her about this.
From Charisma's perspective, I can understand her point of view. She'd had a lot of problems getting pregnant and had a few miscarriages. It makes sense that she would want to make sure that this pregnancy was going to be okay before she told anyone. But, from a employment perspective, it might have been a better idea for her to at least tell Joss as early as possible, so that he was able to come up with an alternative storyline, if the pregnancy progressed. God forbid she miscarried again, she would have still needed time off to recover from that, so the scripts would have to change anyhow.
I read somewhere that it was because Charisma miscarried that Cordelia and Groo took off in the middle of S3, but I've never had that confirmed. Anyone have a link or something to that?