I agree with Shadowkins. Give her some time. She has just been through a very stressful experience. Your reaching in too her crate she probably associating with the vets office. The vet tech, ie. a stranger, reaching in to her kennel scared her and that was followed by every scarier things. When you reach into her crate it reminds her of that. Being held may also be triggering bad associations.
It is really, really hard to keep cats from jumping up on things. That is what cat do! They jump. It's like try to keep a dog from licking!!! If you are really concerned about it, you could try keeping her confined to a room where there is nothing to jump up on when you are unable to supervise her. But like I said that is difficult. There are always things for cats to jump on. I was never successful with that with my two girls. Or the boy.
Keep an eye on her incision though. If it is red or looks infected take her back to the vet. Cats are notorious for hiding illnesses and injuries. You just have to keep an eye on them.
Just pet her calmly with a soothing voice. She will come around. Give her some special treats. Treat her like special girl, while keeping all four paws on the floor.