What is really overpowered is friendship. Just imagine, someone with the unfair ability to be able to tolerate or even enjoy the company of others to the extent that they could get other people to want to group up with them. Now that's scary. You come across a multiboxer and you start scattering or CCing their guys, they lose their mind looking at their 4 different computer screens where 4 different things are happening, and trying to get everything back together. But four nerdy friends with head sets, you'll get eaten alive if you accidentally stumble across them on some planet in the middle of nowhere.
Personally, I don't have the ability to tolerate other people on mmo's enough to want to group up and wander around with them for very long, and I'm kind of upset that there are people with this unfair advantage. Still, I guess everyone has their unfair advantages.
Most mmo's I think tolerate multiboxing because they know it's only secondary to the gross overpoweredness of teamwork.
As a side note, I've casually dual-boxed before, and it's really really hard getting all of that set up, getting everyone to do the same thing at once, and while sometimes it's awesome killing guys at double speed, you can barely control either character, and there are a lot of situations where you get hung up. It's a different form of gameplay, and it takes as much if not more skill than playing one character. And it's not necessarily more fun.