Rust HAS to go. First off, it's rough, if you paint over it, the paint is now rough and rocky and all you have is painted rust. Second, rust is there if you paint it or not, you want it gone, so you sand it. Obviously some rust is extreme and metal has to be replaced, but yours doesn't sound like that.
Also, last I remember, most touch up paint is cleared already, but in my experience, touch up paint really in the end just sucks. If it's just small dots, go ahead, if you're missing chunks of paint (think half an inch or bigger) you're getting to the point that said panel/area needs a repaint.
