Given the situation (and if it was one of the guilds I'm familiar with that you're in, Gareth, these are pretty much non-PvP guilds, with an emphasis on roleplay) i'd say you were 100% justified. This kind of behaior isn't excusable. There are three situations I will attack a guildmate: (For those not familiar, my guild is actually affiliated with some of Gareth's, though not officially allied anymore)
1) In jest, running around, I might tap someone and run. "Love tap". I don't ever attack to kill. The other day we did a little dueling, but it was all consensual, and any kills were purely accidental. Had anyone at any point said stop, we would have done so
2) Scripting or unattended macroing. Just no. Not cool. The only reason I'd loot in that case is to prevent them from losing anything on their corpse, which would be returnde.
3) To defend another guildmate or alliancemate... if this situation happened in Dragon's WAtch, you can damn well be sure I'd do that. Well, I wouldn't have to... I'm an emissary, so I could have just kicked him.
However, I do want to know; if the other emissaries were online, and just on alts... why didn't they log and switch over to an emissary? I don't think you were in the wrong, but I do have to wonder why they didn't just kick him if they knew what was going on.