Mother squirrels will only kill if she cannot care for all her babies. She will kill the smallest of them and continue to kill until she thinks she can care for the rest. It is just the way of survival for them.
Like almost all rodents, if a nest is distrubed and the mother thinks the babies are lost, she will eat the babies to recover the calories expended on the babies.
I think they only kill the weak ones, it is because they don't want weak ones in the bunch. It probably would be able to take care of it's self when it gets old enough to.
