Well, I do agree that people that are good at the task of hacking should get a reward, but I don't see how you can prevent people from abusing that system. Maybe that's why it's so simplistic now?
Maybe we could use a mix of point system and puzzles, or some kind of challenge to even the playing field. Or maybe you could get a choice of which one to use when getting your hacking kit?
Each person could choose whether they would like to use the point system (which because it requires more time, could lead to a higher reward), or they could do a puzzle (which could reward with faster time for faster completion, but wouldn't get quite as fast as the point system).
Maybe the choice would alleviate everyone's dislike of the other side.
If anyone has any ideas please post them. I can't quite come up with a system that makes everyone happy.