Hi Julian,
Here's what I did. I took the quarter glass, the rubber seal pieces and the frame pieces to a glass shop and had somebody who knew what they were doing do it!
At least, that's what I think I did - I don't actually remember.
It's something that if not done right will be ugly and obvious. Unless you have enough of the rubber seal to experiment and make mistakes, I would advise you to you my method.
Of course, if you are more adventurous, a long way from a glass shop, and/or poor, I would get the sharpest razor knife I could find. Carefully mark the line you want to cut (as you say 1/2 the angle). Find some way to support the seal so that it doesn't move and is close to the position it will be on the car and make the cut using a metal straight edge. You might be able to employ the quarter window to support the seal when you make your cut. Obviously, you don't want to scratch your glass so maybe you could use a piece of plywood in place of the quarter glass.
Good luck!
(Ok, that was a welder and not a glass installer, but I thought it was in the same spirit!)