I think this is an excellent idea. The possibilities are endless for a system like this, but I think a more focused approach could bring a more meaningful experience to being a part of a guild.
Many MMO's developers have forgotten the importance of player interaction (both negative and positive) in the games we play. They censor and separate players to promote a "positive" playing experience and diluted the true social dynamics of MMO's. Guild quests promoting "positive" (grouping with guild mates) or "negative" (PvP or GvG combat) player experiences could only help improve any MMO become a more social experience...the way they were originally intended to be.
Too many games today have forgotten the wonders of playing with people from all over the world...or even your next door neighbor. Systems like these could help players re-experience that wonder. Even if it's only on a smaller scale. Being in a Guild should have meaning beyond an additional nameplate. Guilds and Guild Quests could truly help put the "Multiplayer" back in MMORPG.