I think this kind of problems will always haunt Minecraft and its mods because of its player base.
Minecraft is a really kid friendly game. Its mods will give it longevity unparallelled by almost any other game there exists. It can be played alone or with friends, and in almost any way imaginable.
These factors make the game really popular, and it draws in a lot of kids or early teens with little to no experience on the Internet, and with manners and behaviour according to their age group. There will, at any point, be a ton of immaturity around. These people have yet to learn the social codes of (proper) online gaming or the etiquette of forums. All they want is to have fun, without regards to how their definition of fun clashes with other people. A moderator or admin is just viewed as a person with awesome powers that can be exploited for extra fun. It's a nightmare to moderate and administer.
More mature or grown-up players make less of a fuzz about themselves. They play by the rules, and use the chat as a secondary means of communication (using IRC, Skype or something similar to communicate with their friends), they know the codes, and they know how not to be annoying. A good user is usually a silent user.
This means that the chat often will be left open for the inexperienced. The more modest users stay in the shadows, leaving the chat to be taken over by the kiddies. At a glance, it will seem like the server is flooded by idiots. Usually, though, it's a case of a vocal minority, and they are vocal because they don't know better. The same can be said about certain forums.
Personally, I like to close out "the mob" and play locally hosted games with a couple of friends instead. Eventual idiots can easily be kicked out of the game, and then given an IRL whack if needed. It's OK to play with inexperienced people, but ideally you want to keep their numbers low (ideally, just one "newbie" at a time), and keep them close (preferrably in the same room). That way, you can teach them things quickly, and they can ask silly questions without bothering the entire server.
