Hopefully you have a dry indoor space in which to work. Have the windshield removed, or do it yourself (it's not that difficult) then you will be able to see the extent of the problem. After the glass is out, you will need to remove every trace of the old adhesive from the opening. Tape a drop cloth in place to protect the dash and seats. Scrape as much as you can (try not to go through the paint) then use solvent to remove the remainder. (do this outside if at all possible) Of all the things I've tried, carburetor cleaner seems to work the best. Spray it on a rag, then wipe---don't spray it directly on the goo or you willl have a horrible mess. After the area is clean you can deal with the rust in the usual manner. Hopefully it is only surface rust. Large areas of missing metal would strongly suggest looking for another car, as welding is impractical in this area without A LOT of difficult and time consuming trim removal. Assuming it's not the worst case scenario, and you are dealing with surface rust, scrape off any loose flaky bits, then sand the area with medium (80-100-120) grit sandpaper. Depending on what you are going to coat it with, you may need to take it down to bare bright metal.(if using regular primer) If you are going to use POR 15 or a similar product, some rust can be left, as long as it is smooth and solid. Top coat with paint that matches the rest of the car. If your car is a metallic color the repair is going to show to some extent, as you will probably be brushing the paint on and the metallic particles won't align properly. After everything is fully, thoroughly dry, reinstall the windshield.

If you have to drive the car to and from the glass shop with no windshield, (not a great idea) open all the windows and go VERY slowly. If it's a wagon, prop the tailgate fully open. There is a risk of blowing the back window out with too much air pressure. Better to take the glass out yourself, do the rust repair, then pay someone to come to you to put in the new one.