It's such a horrible situation and there really is no happy outcome so you just have to choose between the lesser of two evils. I know at my shelter they abort if the mother isn't too far along. They hate it too but what solution is there? They had one the other day that came in and I was holding her and I thought she felt pregnant. I told them and they had the doc check her and she determined that she was but not very far along. When I came in the next time the director was very upset. They took the kitty to surgery to spay and abort and found out that she was much further along than expected. Of course it was too late for the kittens but there were tears shed for them. The vet was in shock because she couldn't believe how starved this poor young mother was. She was so skinny that you couldn't even tell she was on the verge of giving birth. It is simply a very very sad reality.
Good luck to you with whatever you decide to do and please keep us posted.