I'd get the male neutered ASAP, if it isn't already too late, then you can spay the female after her heat (cats can be spayed while in heat, and even while pregnant, it's just more difficult and expensive, but there is nothing at all to stop your from neutering the male now...it's also cheaper than a spay...and cheaper than kittens).
My concern isn't that the cats are related, it's that they could mate, period. I see way too many unwanted cats and kittens to say otherwise. Kittens are expensive to raise properly and with adequate vet care, so plan ahead for several more spay/neuters, vaccinations, and vet care if kittens do come. How will you pay for and home them, and what will you do with any kittens that don't find homes or that have major medical problems? Those are all valid questions to ask before you knowingly let your animal breed.
Separate them at all costs and at all times, in different rooms with the door securely closed. You'll just have to spring for another litterbox (again, cheap compared to kittens) and keep them completely apart until one or both is fixed. Be prepared for some acting out, crying, caterwauling, urine spraying, scratched doorways, and broken knick-knacks along the way, as a female in heat will do anything to get to a male and vice-versa. It will be unpleasant, to be sure, but it beats a litter of unplanned kittens.