Many years ago we had two kittens who had been foster sisters, so they were not quite the same age – a couple of weeks between them, I think. When they reached their first birthday we made arrangements to have them spayed. (In those days it wasn’t advised for females to be done until they were a year old.) The slightly older one had shown some signs of coming into heat, but the younger one hadn’t.
When they were under the anaesthetic the vet discovered that the younger one was pregnant. We had no idea – we had no reason to suspect that she might be, but by the time it was discovered, things had gone too far to save the kittens.
I confess that, had I known, I would have let her have her babies, and then the op afterwards. But honestly, she showed no sign of having been aware of them, and certainly didn’t appear to suffer in any way from their loss.
In your situation, knowing that any kittens born to your cat (still a kitten herself!) would be very unlikely to have a happy, healthy home life, I believe that it will be kinder to let the vet operate. Yes, you will mourn their loss, but you can be sure that the babies didn’t suffer.
It’s such a hard and painful decision for you, I know. Try to accept that the cat you know and love will have a longer, healthier life after the op, and be glad for her. Unless she is near the time of delivery, I don’t think she will know anything about her kittens.
I’m so sorry you have to face this decision – please don’t blame yourself for whatever happens now. You can only do what’s best for your cats.