I'm completely pro-pvp, but I don't think it should be implemented in the form of specific areas of the game or instanced off. It should have its own server with rulesets that vary, maybe just start off with one level-range FFA server and if it gains popularity then go from there with more servers with different rulesets.
In any game that has instanced off PvP like BG's or zones that are dedicated to PvP, it becomes nothing but another grind for honor points or banana stickers or whatever the little token may be. The best PvP has always been in 2 forms, either a game like DAOC that is designed from the ground up to be PvP based, or like it was on classic EverQuest/Project1999 Red today and vanilla WoW(back in the days of raids on southshore and crossroads).
The reason behind this I think is that when you have a game designed for PvE like EverQuest/Early WoW/Pantheon and you open up a PvP server that is basically just the regular game with PvP switched on, it for one clears up most of the issues with the camp "lines" and other player disputes of the like, it keeps the PvP oriented players out of the PvE-only players' hair by keeping them on a separate realm, and it also provides a more dynamic and dangerous feel to the game. After all another human is the most capable opponent that you'll find in any MMO. But most importantly I think that making players create and resolve their own conflict adds a whole different dimension to the gameplay that you won't ever achieve by saying "here this zone is where you fight, this is who you fight, and afterwards you get a shiny and a sugar cube."
Ofcourse some adjustments need to be made, and a big reason why PvE-only players would be against a PvP server is the possibility that the game be balanced in favor of the PvP players which could screw up the way some classes perform in PvE. My idea to prevent this is having the abilities effect players in a different way than mobs, so you can adjust damage/duration or whatever you need while leaving PvE'ers classes completely intact. In my opinion no content whatsoever should be developed specifically for PvP outside of adjusting the abilities as I mentioned before.
But I think that PvP definitely should have a place in Pantheon as long as they leave the PvE servers out of it, and keep the PvP on the overworld and let the players decide who to fight and why to do it.