i have bred mice for a while and have never had a problem with touching the newborns and the momma eating them from the smell. I think thats just a bird thing honestly. When i clean my mommas cage i move the nest around and clean around it. mom doesnt' matter, all of the moms don't mind. How many litters has that momma had? if its the first or second its pretty normal for them to do that because they get so overwhelmed