I like this post over at I am a Paladin -- it's a pretty insightful look at why drama is so easy to come by in bigger guilds. Blizzard has done almost everything they can to divide loot fairly (and they're still working on it, with the addition of more token systems), and there are certainly plenty of systems out there to try and keep things as fair as possible. Still, as long as there are only a few rewards to split among 25 people in a raid, there will always be loot drama -- as IaaP says, when people aren't rewarded for their hard work (or at least they perceive that), then frustrations start to set in. And gone unchecked, that can lead to jealousy or resentment, which leads to anger, and that all leads to the kind of spectacular guild breakups you can read about in Guildwatch.
So how can you avoid all that?
If the main reason people start causing drama is that they don't feel rewarded, then you've got to find a way to reward them. That might mean going with a more fair loot system (I've been in a few guilds that have switched to DKP at the first hint of drama), it might mean changing up the way you run things (by switching groups around or switching roles in a raid), or it might mean stepping back down into an easier raid to better gear up some of your members.
As long as Blizzard requires more members than loot in a raid, there will always be imbalances, but hopefully most drama issues can be avoided if everyone realizes that though any given piece of loot might get passed out unfairly, there'll always be enough to go around.