Well, my little girl was subjected to some flash at age 10 minutes, she's fine. She actually likes it, and poses now whenever she sees the camera coming her way at age 7 months. (I kid you not) I'm talking on board flash from a Canon G10 though, turned down a notch or two. Not a 580EX2 on full pelt!
However, if you really want good baby shots I don't think you can beat natural light, and maybe a bit of reflector for fill. I'm no expert but got good results this way myself (or at least I thought so)
I had to bump the iso up a bit but there again there wasn't a lot of light at the time, in a bright room you wouldn't have to as much.
Ste