There are two ways to go about it, for one thing - if you don't go to Felucca, you can't be attacked under VvV rules. That being said we are also looking at an individual opt-in/opt-out for members of a guild. However, if you were opted-out of VvV and you enter a battle region you'd be fair game.
We are still working on it, and thanks for the feedback!
It would make it so much more useful for most guilds if there was an individual opt-in/opt-out for members of a guild. It would help building the community, when a guild not have to be 100% PvP or 100% non PvP and a lot of the hate between PvP'ers and non PvP'ers will die.
I tried to make a separate guild for the factions players. It did work as long I could ally the guilds but after that become impossible, it killed my guild. It did not get better, at the time where the factions items was more powerful than crafted and farmed items.
A guild work best if the members need and support each others. PvP'ers do not want to use a lot time crafting or farming but they can protect the crafters and farmers in the guild, if they need to go to Felucca for Power Scrolls better resource spawn.