I would like to suggest perhaps a veto system. Any member can call anything major (minor things will not be voted on) to a vote - say the main villain. Majority will win, however every member gets one veto and can veto the idea if his side loses the vote. Vetos could not however, keep something in. Members would have to respect the veto.
It's just an idea, but I think it is a good one. Of course, there are downsides to such a system - it can cause tension between team members if someone vetos someone else's idea, etc... but I think that any guild member should not be forced to go along with a major idea if he feels strongly enough that it is bad, and I think the veto system would address that. Of course, I am open to other suggestions.