How do I fix this mess??

Apparently Tinyharts had some cage security issues earlier this month. They have most certainly been remedied, but not without some consequences. I found a little pet type brindle doe of mine wandering around. I'd decided not to breed her as her type was terrible, she is tiny, and her color moulted into something very uccky. At around the same time, my import-derived agouti boy went missing. I finally caught him two days ago.
Well, the little brindle is very pregnant now. I don't know what fathered her litter. It's most likely the agouti buck, which I don't mind terribly, but he is A/A, like a wild mouse would be. SO basically the results would be similar and I would never know who the true father was (until I had potentially insane weanlings). If I am not mistaken, I will probably get brindles and agoutis either way. It could have also been any of the boys who hang out upside down on their mesh.
Basically, I don't really want this litter. How do I proceed? I want to do this in the most ethical way possible.
I want to stress that the cage problem's been solved and this is a big embarrassment to me!

In my opinion cull the litter at birth, as soon as possible to reduce the strain on the mother. She should recover quickly once the pups are culled.

Thank you Cindy, I see your response on here and another forum! Thank you!
Will the doe get infected or is there anything to watch out for? Also, tell me this sort of thing happens to most...

Infected? If you have wildies, she could get parasites or diseases from them, but culling her litter shouldn't get her infected with anything. Mastitis is a possibility, but unlikely.

Mastitis is very unlikely, the main purpose of culling at birth, or soon after, is to further decrease that risk.

Agree with culling at birth. Easiest way to handle the situation and less strain on mom

I ended up keeping three does because I noticed that they are especially placid and have lovely typey skulls. I am thinking that the import agouti is the father, in which case, I'm happy to keep them. I am thrilled that it was soooo easy to tell the difference!!!