I think they would have killed her or at least put her in a coma anyway. But I do think it could have been better, simply because we presumably wouldn't have had Cordelia/Conner.
Plenty of shows accommodated the pregnancies of their actresses. Holly Marie Combs (Charmed), Lisa Kudrow (Friends), Caterina Scorsone (Private Practice), Jane Leeves (Frasier), Debra Messing (Will and Grace).
It's a pretty common thing for long running shows that cast actresses in their 20s-early 30s.
I have a hard time believing that Charisma wouldn't have said something if she knew she was meant to be the seasons big bad. Like Lyri says, she probably had no idea. And if that is the case, then you could argue that the "you should have told me sooner" thing could really work both ways.
It seems that Joss got mad at her and unfortunately I think he let that come through in the story... which in my opinion is one of the worst, most unprofessional things you can do on a show.