Do male rabbits kill the babies?
Do the males kill the babies? And should the males be separated from the babies right after birth?
We don't have any experience with leaving male rabbits in with the babies, but from all we've heard and read, the males don't typically kill the babies. In fact, we understand that they can be quite solicitous of the youngsters.
(Perhaps if others have actual experience, good or bad, they'll speak up...)
But there's another reason why you might want to remove the sire - he'll be only too happy to rebreed the doe within 24-48 hours of delivery. That's what happens in wild rabbits so it's a natural behavior, but, two litters back to back may drain the doe's reserves. If it happens, just give the doe a break before the third litter, so she can regain her weight and condition.
Good luck, and enjoy!