The good news is that lots of guilds have been through this before, and there's a lot of great guidance out there about how to switch to DKP and what kinds of systems you might use if you do. I've only been in one guild that decided to go from a free-for-all roll to a loot system -- they chose Suicide Kings, everyone agreed it was fair, and they've never looked back. Donnyman's having an issue with his guild leadership's decision to put a little erosion on the DKP, and it's true -- if the whole guild isn't behind a disagreement like that, there could be some breakup. There's lots of great discussion in the LJ thread about how decay actually affects people who can't raid from time to time, and Donny ends up with two choices: be OK with it, or find another guild (there's plenty of them around).
It's not impossible to pull off a switch to DKP from a free-for-all system, but you need to a) make it clear that it's in everyone's best interest (if loot drama is starting to sneak up, it probably is), and b) make sure it's as fair as can be. Consider what your guildies want (more loot, just to have a good time raiding, or to reward people who do well or people who need the gear), and then go with a system that meets those needs.