She doesn't quite look pregnant to me, or if she is, it's really early.
We added a bunch of fake plants in our tank to raise them in the parents' tank, it's a lot less stressful on all of us, and the parents do their own culling of any sickly ones.
Your babies will be fine in there, they won't stress mom out at all, plus, guppies don't like being alone.
Have you tried contacting a pet store to see if anyone would take them in? I would take them, but my fiance is trying to get out of fancies and into commons. >_<