In the overall scheme of things, it's a minor setback. You are taking excellent care of this little girl.
I don't think the infection is a result of how you did the surgery or post op care. I believe her immune system was severely taxed from her long battle with her crop and gizzard issues, so by the time you did the surgery, she didn't have many defenses left. But you've been on your toes and alert for any complications. It's darned handy you had the Baytril on hand.
I think in the future, I'm going to recommend an antibiotic concurrent with crop surgery. You wanted to do that, and I should have said, "Good idea".