I would sand or scrape whatever rust is there, then neutralise it with a rust converter. Fill the spot with a dab of primer with an fine artists paintbrush. Follow up with basecoat then a couple coats of clear allowing sufficient time for each coat to dry.
Then rust converter, primer, paint etc as above.
Rust converter, primer then multi layers of paint in a hole <5mm in diameter and with modern paint being less than 0.1mm deep is practically impossible.
As long as any surface rust is removed, and the bare metal covered with a touch up paint then corrosion is going to take years to come back if at all
(* I've done multiple stone chips this way on both of my current cars, and have had no reappearance of rust ~3-4 years on)