Fish are oportunistic, if it fits in their mouths it will likely get eaten..
That being said. Provide plenty of cover if you will be keeping fry in the community tank..
I am a fan of a nursery tank myself.. I am not into guppys, but if I were, I would pull the mama & still provide plenty of cover in the nursery also. This way mamma won't concider them lunch (as much). Remove the mama ASAP,.
I recommend using common water in the nursery. I use main tank water for partials. until I devise a plan to comingle the water. I have a plan, just not the time to put it in place just yet. Have to build a special stand.