I would - sadly - expect this to get worse before it gets better (if it's going to).
Your puppy is as the most maleable age right now. They are as accepting of everything around them as they are ever going to be. That doesn't last. As they mature, they start to learn ways in which they can make their feelings known and, if they have experience with someone who they found scary and stressful when they were a puppy, they are likely to try and communicate that as they grow up: with side eyes, freezing, avoidance leading to growls or snarls or snaps or bites.
That's what you have to guard against right now. If this puppy is to have a chance of growing up to accept your daughter then you need to control every interaction right now so that he does not get hurt or scared by her.
Through the teenage months, dogs can be irritable and intolerant and downright little arseholes. They really can test even the most patient of adults: chewing, zooming, biting, refusing to listen, barking, digging etc So, beyond the puppy years you've got about 6-12 months of that to get through also. Again, your role will be to make sure neither your dog or daughter do anything that could sour the relationship between them for life.
Much better they ignore each other for the first 2 years then grow to accept each other later on, than they are given too much chance to interact without lots of help and do something silly that means they never grow to accept each other.
Sadly, your beeder is also a dickhead. No decent breeder ever refuses to accept back a puppy like this. Ever. So you may have to handle poor breeding (health and temperament) into the mix.
It sounds like a huge undertaking, to me... Sorry OP.