smitchell,
Oh no, not the door panel!! I misunderstood you I guess. The "heads" must be stripped out, but the screws/bolts are in one piece. If it is a raised head screw and you can get a nice new, sharp pair of vise grips on it, that, combined with a little heat and some PB Blaster or other penetrant sometimes works.
If it is a flat head screw, which it probably is, I would customize a screwdriver to fit the buggered up head, apply some pinpoint heat with a torch, let it cool a minute, squirt it with WD-40 and give it my best.
If there is any head left, the impact screwdriver works well, but you mentioned the fact that the glass was still in the door. Glass is pretty tough, a smack with the impact driver probably wouldn't break it...my secret is always heating the fastener red hot, let it cool a bit and shoot it with penetrant. This breaks the bond between the threads and the screw.
Stuart.
