Repair a Few Tiny Pinholes in Windshield Gasket Channel?

The only way to stop it from rusting is to cut it back to good metal and replace it, anything else you do is a temporary fix. That doesn't mean that your temporary fix won't last for years if you do a good job of it, but it's still just temporary.

If all you do is clean and fill it, it will continue to rust. You can't neutralize everything between the layers of the metal unless you cut it apart and replace the bad metal. Maybe that's not what you wanted to hear, but that's what'll happen. I wish it was easier too, I'd have a lot less metal to replace on my cars, but that's just not how it is.