I'd take one bolt out at a time so as not to disturb the fitment, clean up with a wire brush on a drill,prime and paint....if you want you can bolt it back in before you put the top coat on so as not to risk damaging the paint
For that specific situation, I'd shield the surrounding components so as not to scuff anything, clean up the rust with a very small wire brush, then use rust converter and touch up.
I dont see a need to remove the bolts or replace with stainless ones.