I'd do as you said, keep them separated when you are not home, especially as you do not know which dog did it, for sure, or the circumstances. I'd call you vet now and schedule an appointment to get momma spayed after the kittens are weaned. If you call now, they can tell you when it would be safe to get it done and get it on the calendar.

Do not feel bad, you could not have known, okay?