Most shops will not touch rust, including the one I work at. We just did a VW rocker replacement for $2800, and it still needs the other side done, we did it for a long time customer. And it was "a deal". A ton of work to do right, and it'll probably return eventually.

I'd try Rust Repair Inc like someone else mentioned. You're probably looking at at least $1K to paint the rocker and blend the quarter panel.