On the front window you can probably get away with applying some Picklex 20 over the cleaned up rusted area then epoxy primer then a little fiberglass paste to fill the holes then paint before reinstalling the glass and moldings.
On the back window I would remove the glass and replace the rusted metal by welding in new metal then epoxy prime and seal it with a "good" urethane sealer then paint before reinstalling the glass and moldings.
Note: I would recommend reinstalling the molding clips before reinstalling the glass, it's a lot easier than putting them back after the glass is in.