What should I do with these puppies?

My granny’s female dog is pregnant,the matter is that it’s done by her own brother(from the same litter). I know we should separate them or at least neuter him,but it’s just too late. I know her offspring will inherit some genetic problems but we don’t want to do abortion (that’s too cruel!),and I also heard that gene therapy will cure this problem. Is there anything we could do to solve this problem?,What will you do if you’re in this situation?.