If you grind the rust back and treat the area really thoroughly you should be alright almost permanently with a really good quality filler.
I've got the classic MK3 rust spot (about 2 inches long X 2 inches high) on the bottom left-hand corner of both passenger and driver doors (3 door model). Drainage holes in the doors are clear but the evil rot has got in anyway.
Its not a repair, it's a bodge. The only way to repair rust is to cut it out and replace with fresh metal, otherwise it'll just keep rotting out under the filler and spread. This is why so many mk1s, mk2s, beetles and buses are sh!t boxes