This is the only way I can imagine you could do this without paint. Get a window and make a channel that would go around the window. Cut a hole in the body the same size as the channel, we are talking PERFECTLY cut it out and grind it out to the perfect point. Glue the channel to the back side of the metal with structural bonding adhesive. (YES it would be strong enough) And then set the glass on urethane in the channel and use a moulding like on an 80's S-10 Chevy or Camaro of the vintage. The moulding simply tucks into the channel between the glass and the channel sealing over the gap between the glass and the channel.
You may be able to pull this off without damaging the paint.