My dad taught me how to do a lot of fiberglass work for restoring my CR-X. My quarter panels were rusted out so bad I could stick my fist through it, and I wasn't able to safety the car until it was fixed. I know yours isn't nearly as bad.
The best route to fixing it would be to use a grinder, and grind away all the rust and surrounding area (at least 2 inches around). Don't use Bondo for smoothing it out after, 'cuz Bondo is shit. Go buy a fiberglass kit (very inexpensive) and plaster some over the grinded area. It can be uneven since you just have to sand it smooth after. Just make sure there are no bubbles!
You can take it to a shop after and they can prep and paint the car for you. If you are wanting to do it yourself, I could give you some pointers, but keep in mind it's a lot of work.