I replaced the glass in mine, but it was NOT easy. I asked the same question as you when I started. The best suggestion I received was this:
"I have lubed it with WD40 & tapped them out with a rubber mallet, tapping them on the edge of the glass."
This process worked fine for one of my quarter windows, but the other would not budge. I figured that I didn't need to keep the glass, so I simply put the quarter window (complete with glass, bracket and molding) into a thick bag. I sat the bag on the concrete and took a hammer to the glass. The glass shattered into thousands of pieces. I was able to pick the remaining shards from the seams with a screw driver. I refurbished the finish on the stainless and inserted the new glass. Oh -- and I replaced the seals on both with a thin rubber tubing-like material.