As Drysc said, the problem isn't just a matter of punishing people who break the rules, it's finding out why they are doing this, and change their incentives, so that they don't want to break the rules in the first place. Our reader Aviel has some insights as to why people AFK and how to fix it, and she (or he) has posted her excellent analysis on the official WoW forums.
In short her argument is that, while Blizzard is trying to develop PvP content that is "fun, competitive, and compelling," players are generally making "game theory" decisions, about how to maximize their honor gain in the time they have to play. Fun is definitely an element, but overall, if people can't earn enough honor to make their time worthwhile in a particular battleground, they will quit or seek alternatives. She points out that as long as honor is a kind of currency to be spent, people will choose the method with the easiest honor gain over the one they enjoy most (which can lead to get-rich-quick schemes such as AFKing). She leaves her solutions to this problem for the Suggestions forum (though I could not find her actual post there), but posters in that thread share some ideas, and there are many other player suggestions out there as well. Of course Blizzard is tight-lipped about their own solutions so far, but we can rest assured that they care about the issue and plan to do something about it.
I agree with Aviel that most players are evidently seeking the fastest way to get honor gear over the best way to have fun. But trying to earn honor currency in the fastest way possible is itself its own game-within-the-game, and the drive to earn as much honor as possible by winning can be a great motivator to do one's best. Clearly the temptation is very strong for AFKers to try to scam the system and get something for nothing, but I would hate for the AFK problem in Alterac Valley to require that we give up honor as a currency, or heaven forbid, force us back into the old honor system. While it may be true that "love of money is the root of all evil," just getting rid of money can't fix the problem of human selfishness.
The honor economy must revolve around justice, so that if you want to spend honor you can work to earn it, but no effort also brings you no reward. The system should allow a good deal of freedom in how you choose to earn your honor, but no freedom to leech it off of others. The question is: how can such justice be achieved, especially in the face of the selfishness that inspires AFKing?