It would help to know how old the babies are.
If you are keeping the babies separate from the mom its important that they have access to her cecotropes and poo so they can eat it and get the right gut bacteria from her. So, if she is attacking them and kept separately I would take her out of the cage and let the babies go into her litter box and let them help themselves.
First besides pellets, I would make sure they always have good hay and water at all times. Then as far as pellets go, I start putting out a couple table spoons of crunched up pellets at around 3 weeks and let then nibble them a little bit, I see them nibbling and eating little bits of hay the rest of the day, and they begin drinking water which I leave in a shallow bowl and I also put a bottle of water on the side of the cage really low so they can reach the spout. I think if babies are eating dry food they need to be also drinking water. You can increase pellets as they get older. I don't quite feed all the pellets they can eat, because I want then to eat some hay as well, I feed pellets in the morning, by noon they have eaten all the pellets so then they have to eat their hay until they get more pellets later that night. I introduce greens by giving a blade or two of fresh grass at 5 weeks which is what the mother eats everyday. But I only give a blade or two of grass to each baby just to introduce then to eating greens. By 7 weeks they are eating pellets, hay, 4 or 5 blades of grass, a dandelion leave and a sliver of carrot. I've had about 8 litters so far and they have all lived. Haven't had any enteritis.
Whether you have the mother feed them depends on how old they are. I would keep putting mamma in with the babies like you've been doing until he babies lose interest or she goes dry. If the doe is full of milk it actually is really uncomfortable for her if she can't get rid of some of the milk, so people wean gradually not only for the sake of the babies, but for the sake of the doe.
