That is a quite common combination, but there should be some proper bonding done. When just putting them together it's pretty normal that one rabbit gets chased. That's part of sorting out who's boss, taking into consideration what makes bonding easier like neutral ground can reduce the risk of a fight. Also when they have enough space so that either of them can get away and hide. Some chasing, humping and even tufts of hair flying can be part of the process.
It's not that hormones make does fight. Hormones bring mood swings, and all the natural behaviour. My spayed doe attacks unfamiliar rabbits that venture into her and her bucks territory too.
Why would she hurt the babies? No. My breeding does live in pairs, I don't know for sure how a neutered buck behaves around a nest, but with a dominant doe I would think it should work. Maybe seperate for 2 days around kindling, but with exercise or garden time together (I do that sometimes with my does, just to give them some peace, rest and privacy)
They'll need quite some space, I connected 2 hutches with tunnels, so if one doe has kits or is in a bad mood the other can go out of sight to the other hutch. No problem in 7 years with 2 pairs.
Rabbits are social animals, I enjoy them interact so much that I'll never keep a rabbit alone again, if it can be avoided.