Hate to say it, but the only way to correctly and successfully get rid of that rust is to remove the screen and rubber seal and repair it with a weld and treat it from inside so the rust doesn't come back.
Removing metal, treating and filling with body filler and POR15 still won't cure the surface rust that's on the other side of that panel.
I have an 89 VW Caravelle, I do what you're doing on an annual basis, because I can't be bothered removing the glass and fixing it properly. Some of my work lasts for more than 12 months, some less, and there's always a new one that appears not long after you've fixed the rest. I remove all the flaky rust, apply the metal ready, then the POR15, then a tie coat before filling the hole with whatever filler I have to hand. I then apply another POR15 over the finished fill, then prime and colour as required. The rust still comes back..... I don't have that much time to spend on it until I slow down my work week. Otherwise I'd be doing it once, and properly.