To be clear, by "genital mutilation" he means "male circumcision", which is incomparably less bad than female circumcision, which is what the term is generally reserved for.
Male circumcision = cutting off the foreskin, which is not a procedure I'm a fan of, but is still performed on the majority of Americans boys, and is fairly harmless, in addition to potentially reducing risk of AIDS. Female circumcision = cutting off the clitoris, and has been condemned as a human rights violation by the UN.
It may not be a strictly false statement on his part, but it's obviously a shady, misleading way of saying it. Now if Bill Gates had funded the lopping off of kid's penises, it would be an apt description, and analogous to female circumcision.