Oh my. Liz - so sorry for you and your baby girl.
Strangely, though I mentioned Flower earlier this actually sounds more like what is happening currently with my girl Ripley.
She is around six weeks pregnant and I took her into the vets tonight with suspected pyometra.
He agreed that she has pyo and I've asked him to remove her womb. I would probably not have done that with any other cat - but this is her second problem pregnancy.
If she has pyometra you won't get a live kitten out - they can't live in that environment.
Is it too late to ask the vet to spay at the same time? Because what she's going to do is remove the babies and somehow try to remove the infection (I have no clue how they will do this). Sewing her back up with some infected material still inside her - well I can see why the vet would be worried.
She'll be on anti biotics for a long time.
So sorry Liz.