Well, I think in PvE areas you should be able to see your guild mates of opposite factions. You cant see them in Cyrodiil, but you could see them in PvE provinces, you could group with them to do an instance, not being able to attack them though.
I see this could add more stronger points in socialization in the guild, since your guild can have multiple members of oposite factions up to 300 members max based on the info we have.
This isnt lore breaking IMO either, because you see NPCs like argoninans in Daggerfall territory that actually gives you a quest (based on leaked beta video back in april of this year), so if that happens why players shouldnt be able to see each other and interact with each other without attacking each other in PvE territories.
This isnt gameplay breaker either, since the Megaserver phasing thing gives priority, if I remember correctly, the megaserver will put you with ppl of your guild and friends list first in your phasing.
So what you think? There should be able to see players of oposite faction but at same they are in your guild in PvE territories? Or you think its a deal breaker?