My understanding is that a luxating patella does not hurt that much, just feels odd. Vinnie has had one for years, although it's a grade 1 (according to my vet) and does not require any intervention. I actually did some unofficial swimming therapy with him and it seemed to help (he didn't pick his back leg up as much after we started doing some exercises in the water). I would get a second opinion but also keep an eye on it. I don't know how long you've had Sophie for, but the longer you have dogs, the more you're able to assess what's "normal" for them and what is not. It's sort of an art form
As for the separation anxiety, are you certain she whines/sighs once you're gone completely? I always thought Vinnie had a bit of separation anxiety, as he would bark and whine the minute I picked up my keys to leave. However, I got a network cam to see what he actually did while I was gone and soon learned that the minute my car was gone, he just curled up and went to sleep.
Nonetheless, try to do some things that can help reduce anxiety, which include (but are not limited to) leaving on a TV/radio, leaving a piece of your dirty clothing around, ensuring that she has a nice comfy bed to sleep in, etc.