In an interview with Maximum, Game Director Ion Hazzikostas revealed that Blizzard is working on the tech required for Cross Faction guilds. However, Ion gave no timeframe to when that will happen, but it is something they want to finish before the next expansion.
Blizzard acknowledges the awkwardness that having people from your guild not share the same guild chat, same guild bank, repairs, guild achievements, etc, and it is working on a way to have it happen for those looking for it.
