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.