The factory applied powder coating is useless when it comes down to corrosion protection, which is why so many of these sumps fail. Once it's started to rust, it's impractical to remove all the existing rust and paint, and overenthusiastic derusting could in itself cause it to fail.
I'd not use paint in this application; moisture inevitably gets between the paint layer and the metal and it'll continue rusting underneath the paint, which is why the factory coating doesn't last long.
There are various non-hardening rustproofing products on the market, but smearing it with a high melting point grease will protect it as well as anything. Even just a wipe over with a rag dipped in used engine oil every oil change time will do the job. There's no need to remove anything beyond any obvious loose flakes before applying this as it'll soak into any remaining surface rust and prevent further corrosion.
Basically the same comments apply to the rear twist beam; another well known corrosion weakness. If you're planning on keeping the car, I'd check this too.