Can you partition off part of the coop for the little ones? That would make integration easier with see but can't peck from the big ones. Then as they get a bit bigger make a small door for the little ones so they can get out but the big ones can't get in.
JT
Ever watch a black snake 4' long just go right up the side of a tree? I've seen it more than once on my property, it's a pretty amazing sight if they are not headed for your coop. Do you have any idea how high a mouse, rat, raccoon, opossum can jump? I've seen videos of mice jumping up a 6' tall...