I never separate my mice. Ever. Once I set up a colony of mice they stay together until I retire the entire colony together. The mothers and the father all help out in caring for all of the babies. I've found cannibalism to only be a problem if the mice aren't getting enough food or water, or if they are nervous about their surroundings. For the first, just make sure they get food and water everyday, if they run out of water, even for an hour they can start eating babies. For the second, keep your nose out of their cages at any other time, don't clean as often, and keep them in the dark.

Mice really aren't as tough as a lot of people make them out to be, but people tend to over think and over work the whole process. Often with mice, doing less is better.