No doubt, totally separate them. Even though he is a puppy and his first attempts at mating will reflect he is clueless, Mother Nature will step in and help him put things in order.
If you can separate them now, you might be able to sleep at night. When his little mind realizes what he has in front of him, he's going to let the entire neighborhood know how unfair it is that you've taken away his girl friend.
Also, once she is in full swing, she might declare her love for him and you'll have two letting the neighborhood know how unfair life is.
Hondo Von Dopplet L Bauernhof "Hondo"- GSD
Lilie's Tug McGraw "Tug" - Golden Retriever
Maggie - Mini Dachshund (Rescue)
Lonestar Pivo - Texas Blue Lacy
Ashe - Barn Cat
Katie / APHA