My answer primarily dealt with the fact that guilds would happen regardless of whether Blizzard formally implemented guilds in the game, but that even without them, PUGs would be the same or worse since it's anonymity and lack of accountability that breeds bad behavior. Certainly there are guilds that have members who are rude outside of their guild, but all good guilds that I've belonged to have rules against giving the guild a bad name by being a funsucker. Guilds without those rules don't keep their non-funsuckers long.
Carmelo at Clever Musings has had similar experiences to mine. Guilds for both of us have been places that foster friendships and camaraderie. Carmelo also believes along with me that random PUGs would not improve, but -- unlike me -- thinks that realm PUGs wouldn't improve either as Raid and Dungeon finders make it too easy to group rather than hanging out in Trade Chat begging for more members.
Tiny Priest (beware of NSFW language), on the other hand, agrees with rayden54 that guilds foment bad behavior outside their own people. Tiny thinks that it's popular to denigrate new and uninformed players and suggests that perks be removed from guilds and replaced with a karma system policed and enforced by Blizzard's Customer Service team. A player's perks would result directly from not being reported for behaving like a funsucker and that guild rewards would depend on the karma of its members. The longer the player goes without getting the attention of CS, the more karma points are racked up.
I disagree with Tiny Priest in that I do think this would put too much of a burden on an already busy customer service team and that it would be open to misuse. Funsuckers would just report people according to whim and the wrong people would garner bad karma because of it. A group of griefers could use their numbers to punish anyone who catches their attention. I shudder to think of the consequences. While we would all benefit from greater individual accountability, how would we accomplish that? Janincognito believes that a good start would be making our ignore lists infinite and making ignore account-wide.
Readers Paul27 and Benjamin believe that WoW's current guild system is very anti-guild. Paul27 believes that guilds are no longer groups of friends or people who have similar interests and goals, but instead are huge impersonal groups together only for the benefits. Certainly there are those types of guilds, but there are still plenty of others who are together for the people and the benefits.
Overall, we pretty much all agree that guilds would happen in some form even without WoW's formal support of them. But whether the game would be better without this formal implementation is still up for debate.