A couple of hours of separation will not do any harm, him mating his sister long before she should be and by the wrong male may cause you lots more problems.... you will need to get it sorted asap. Boys are fertile by the time they are three months old!
for this young a kid it may actually be easier for the vet to do it under gas&air in the surgery, and he won't feel a thing. Cheaper for you too, bring him in in a big dog crate.