You do need to separate the pair as soon as you are able. Momma chins can get pregnant again very soon after giving birth, and there have been some sad stories about newborn kits getting squished during aggressive breeding pursuits. Not to mention the fact that nursing a kit and being pregnant again is very draining on the momma chin.
I'm sorry you had a chin mis-sexed - it's a real shame. If you're not comfortable having both sexes, find a good rescue or put up a post in the classifieds on the forum. It's your business what chins you choose to keep, and while I don't support rehoming animals for no reason, it sounds like you're trying to be responsible and avoid this situation in the future. If that means you have to find another home for your boys, so be it.
Make sure your girl is pregnant before you make any decisions.