After 10 years of playing WoW on both retail and various private servers and achieving most of what you can achieve, I decided to start multiboxing a little while ago, and let me tell you, it has been the most fun and challenging experience I've had in WoW. Playing 5v5 arena and winning as one player against 5 others is amazing, and not with the faceroll 5/4 of the same class(shamans) that people usually associate multiboxing with. No, a mixed team and a keyboard filled with keybindings for each separate ability.
Multiboxers get a lot of undeserved flak, I never encountered as many hateful whispers or /spits in my short time multiboxing compared to my 10 years of playing WoW, as others have said in this thread and I'm quite certain it's the case, people hate what they can't do/don't know/can't have. The Fox and the Grapes so to speak.
Some of the obvious options:
1. Limit the amount of characters multiboxers can have(max 5?) - Would prevent utter domination of certain battlegrounds
2. Disable it altogether
3. Disable it in PvP - This has been done before on other servers, multiboxers were not allowed to engage anyone in world PvP or do battlegrounds, they were allowed to fight back if they were being ganked. Was abused to ban innocent multiboxers though.
I personally hope you continue allowing multiboxing.