i think if you separated the boy and kept the girls separately, the boy would be miserable. i'm guessing he's not very old so if he lives to, say, 18, he will be miserable all this time, looking into the cage he wants to be with. chins have been known to stop eating and die over the loss of a mate.
i think you have two options
1. neutering. this is not a decision to be taken lightly. i have lost my boy after a surgery he had to have due to complications after neutering. however, i just had his sons neutered a couple of weeks ago because they were utterly miserable. i thought they'd be ok and i wouldn't have to do it - i certainly didn't want to - but i could not have them suffer all their lives. i knew it was the best choice for them even if it wasn't for me. if you decide to go down this road, make sure your vet is competent, insist on a course of antibiotics (if chinchi had this rather than just a post op injection, he would possibly be alive now), painkillers (some vets don't give them for aftercare) and keep checking for anything that looks different or not right and give your vet a call straight away - quick intervention is very important. both my boys are on a full course of antibiotics, spock even got an additional antibiotic because one of his wounds got a little inflamed. they are both doing well and they should hopefully be fully healed by next check up. they have less than four weeks to go before they can be introduced to the ladies, i cannot wait.
2. keep the boy and the dad together and find them a home with someone you trust. i did consider this option as i very much wanted to avoid the surgery, however, i could not give them away (i don't go on holiday because i don't trust anybody to take care of them!), especially not after i got this rescue girl who was in absolutely appalling condition.
i can't think of anything else. sorry, i know they are not great choices.