I agree your options as it stands depends on how attached you are to them. Female guinea pigs can get pregnant from 6 weeks of age, male guinea pigs are fertile from about 3.5-4 weeks old which is why we recommend to separate male pups at 3 weeks old.
The female may be pregnant so waiting and seeing if she is indeed pregnant and if she is what she gives birth to is an option as well. If by chance she successfully gave birth to a male and some female pups just housing babies with parents would be an option as well. If she is not pregnant, or miscarries/has stillborn, or only births female pups, then having the male neutered is an option. By the time the girls pregnancy watch ends in one way or another the male should be old enough to neuter.
If you do decide to keep both for now and take a wait and see option for what you want to do going forward then make sure there is no way for the male to get back in with the female. Male guinea pigs are surprisingly good climbers, and a determined male can push up a lid on his cage, but can not lift a lid on her cage. And when she goes into heat, which she will if she is not pregnant, or as soon as she miscarries or gives birth, he will definitely be determined to get to her.