Here's another way to look at and use victory hexes.
I play long campaigns vs AI and even starting with a small core the build-up of experience generates force values over 20k. So the same issue about the relative worth of VPs is true.
In the set-up for each battle it is possible to edit the map. I use this option specifically to place victory hexes so that there is a physical objective for me to attain. The random placement tends to put them in the middle of bare patches of ground etc. So I look for map features that make some sense as objectives that a commander might be given. The sort of things I'm looking for are bridges, road junctions, villages or groups of buildings, prominent hills/ridgelines etc. The victory hexes have a symbolic value as objectives which does not rely on the points. In effect I create a mission, "take that hill!" or whatever it might be. Because I'm fighting AI killing every unit is pretty much a given because the AI just doesn't know when to quit. But for me the point of the battle is achieving the mission, and the victory hexes represent the mission objectives. I never look at what the hexes are worth in points, but I sure as hell want to get those hexes because the mission is a 'failure' if I don't, regardless of the score. I also adjust the battle length so that there is an element of working 'against the clock', but without having to do the AI style lemming charge. If I get this right I have to fight an aggressive battle, but not being stupid, to reach the objectives 'on time'. In the context of the long campaign not losing lots of core troops in the process is also critical because I want to preserve the hard won experience. This means it is less fun being a support unit in my army, they tend to be first into danger every time
I don't play PBEM so I don't know if this idea is useful, but if it is possible for both players to view the map in advance then perhaps the mission objectives could be agreed and the victory hexes placed accordingly. If each hex is given max points value and victory hexes are stacked it would also partly remedy the problem of low values because each side could have just one or two victory hexes worth over 1000 points each.
cheers,
Tim