There are products that allow you to paint directly over the rust. POR-15 is one of, if not the, best products out there for this purpose.
The drawback is that any paint applied to only a small section of a panel will always be visible. And this paint is TOUGH. Once applied, it would have to be sanded/ground off completely if you ever wanted to fix the panel to like new. If all you want is something to stop the rust from progressing and look decent from a couple feet away, then this will do the job.
Buy a pint of this- http://www.por15.com/POR-15_Rust_Preventive_Coating
Have your top coat paint ready when you do the job as timing is somewhat critical to getting the top coat to stick. If you let this paint dry entirely, nothing will stick to it afterward.
You can buy small aerosol cans of matching paint at most auto stores or walmart.
Remove anything loose, you can leave any surface rust alone. The paint prefers that surface rust for best adhesion. Paint the area and wait for it to dry enough to get a light finger drag. Time will vary based on temp and humidity. Then top coat. Simple.
BTW, I actually done it to a door panel on my truck as an experiment having used these products in numerous full restorations/restifications/repairs. It works as advertised.