Ok, well firstly, the cone stayed on. She initially freaked out and was flipping all over the place, so we took it off and tried again. Shes not happy, but she is ok, and it stayed on all night.
At the vet this morning, he refused to operate. We saw the proper rat(exotics) vet this morning and he basically said that if we keep sewing her up, the infection will keep breaking through. So she is keeping the collar, and she has 2 kinds of antibiotic and a painkiller to take every day, and the idea is that by next Monday she will go back in, but will probably not even need to be sewed back up at that point, as they heal really quick.
So for now, its trying to drug her without realising, and trying to keep the collar on (il try and get a pic, she looks like the Pixar lamp) and just watching and waiting.
Its a very good thing that she doesn't need another operation just yet. Its good for her AND my wallet.