The topic of intentional breeding is prohibited on these forums, which includes willingly allowing such things to happen when it is in your control not to. For both rabbits’ safety, yes, you should separate them, in addition to eliminating the risk of pregnancy.
What you have is a baby bond. Baby bonds are not true bonds — they are a natural result of rabbits who are not yet in puberty, therefore, urges like mating and territorialness are not present. This makes a great fake and temporary bond between innocent young’uns. It is dangerous because hormones are invisible and you have no idea when or how either rabbit will begin experiencing hormones which will likely facilitate mating or fighting. It could happen when you’re not home, when you’re sleeping, etc.. There are very unfortunate and grave stories of owners who take chances with baby bonds.
Since it is not a true bond, they will not be significantly depressed by the separation. They can still be next to each other with a gap between pens. This is safest. I’m sure they’d both prefer being separated now rather than after a fight happens between them.
Also note that the bond between a fixed and intact rabbit is less stable, for the same reason as a baby bond. There is no guarantee that your rabbits will want to be together and fixing both maximizes the chance of success since you’re removing unpredictable and unstable hormones out of the equation.
For information on proper rabbit bonding, including the necessary preparations that include spaying/neutering, see here: https://binkybunny.com/infocategory/bonding/
The answers provided in this discussion are for general guideline purposes only. The information is not intended to diagnose or treat your pet. Seek the advice of your veterinarian or a qualified behaviorist.