Inner panel how to deal with this rust?

I am curently taking care of the lower bottom corners of the rear windshield, no biggy just some time weld and patience. BUT the front corner got me off a bit since i havent done this before.

I can replace, the window channel no problem, but here is the question for the experts? How do i deal with the rust inside the a pillar.

I cut it open to replace the lower window channel and saw a lot of rust inside. It comes from the hole from the vynil top molding hole at the top of the A pillar.

There is not much only small spots of surface rust on the top of the a pillar.

Also attached some of my rear window fixings.

How do i fix this problem? Any advice would be great, its the only rust on the car.