I'm not really sure that Option 2 is really that much better. A vindictive (or just plain manipulative) player could still abuse that system. I'm thinking (and I'm sure Bill is as well) in terms of Bill's game against WedgeIkari at the GenCon championship which was the 15-5 win by gambit points. From what I understand of that game, one player began the process of non-engagement, to which the other player, smartly, said, well, I'm not going to just put myself out there to get shot. So, in that case, neither player was necessarily stalling. I've had games where I don't think the person was stalling in order to win, but neither of us managed to kill 75 points worth of pieces before time ran out either. So, I think the points thing you've suggest, while a good idea in theory, just doesn't really seem fair across the board. Especially since there's a lot of games that I win at my LGS that I don't kill 50% of the opponent's pieces, but it's because of their slow play, not mine at all. That penalizes me...for winning!
I know exactly what you're getting at, but what I learned from helping my friend James to become a faster player, is that the opponent's slow play can be used as a weapon against them as much as they might be trying to use it against you. The slower they play, the more time you have to analyze all their possible moves, and to know exactly what you want to do in response to them. So when they finally make a move, you move immediately in response and your turn is over in 60 seconds. This puts a lot of psychological pressure on the opponent, makes you look extremely confidant in their eyes, and likely makes them believe they made a bad move since you were so quick to make your own move. Eventually, forcing them to take their turns so close together, they will make mistakes.
Pretty much 100% of the time now, when I play against James, if he's playing slow at all, I know I have him beat already.