I raise rats, not mice, but in the 2 yrs. I've been breeding them I've never had the first male eat a baby. Some moms will eat their babies and sometimes another female will, but I've never had a male do so. Like "Rflagg" said, they usually help out.
As far as removing the male, I've done it both ways and still do it both ways, sometimes. Thinking logically, I can only imagine that continuos back to back litters takes a toll on them, wearing them out faster. I don't have any proof and I don't usually keep breeding pairs around long enough to really find out.
As far as re-introducing a rodent (male or female) to it's colony, I've had good results by placing the one to be introduced in an empty container first, place the original colony in with it, change the substrate in the original cage and place all rodents back in. It's not foolproof but has worked best for me.
It's been my experience that if there's any social problems with male rats not readily taking advantage of a ripe female, the male most likely isn't or won't be a good breeder. A good breeder male should be dominate. Yes, sometimes they'll cower a bit when first being introduced but it shouldn't take weeks for them to be accepted. They should be taking what they want within a day or so.
Now, that's just my experiences and opinions. I'm not saying it's the law.
Take care!
Mike
-----
It is said that 1 out of every 4 people are mentally unbalanced. Think of your 3 closest friends, if they're normal, then it's you.