When I took my doors off, I used an electric drill with a bit that was a little smaller than the diameter of the pin. I drilled the pin from the bottom upwards about 1/8 inch deep. I had to hold the top of the pin with a small pair of vice-grips while drilling so the pin would not spin around while I was trying to drill it.
After that, you can crush the last little bit of the bottom of the pin inward and pull it straight out. I used a pair of electricians pliers to crush the pin all around. Of course the pin is un-usable after that.
At the time when I was redoing my car, I bought replacement pins from one of the repro parts suppliers. The new ones are a little different, their pins are a little longer and have a retainer clip at the bottom so the pins can't fall out.