You can't run Cyrodiil content with differing factions. I think that's about it. I'm in two guilds and no one cares about factions. If several in the guild of the same faction want to do some Cyrodiil work, they get together and do so. So it depends on the content you're interested in and if Cyrodiil is a big part of that.
There's no real (technical) guild related restrictions concerning factions. Like Acadian said, it's only about grouping in Cyrodiil. Battlegrounds and dueling also works cross-faction. So it wouldn't make sense joining a pure PvP (Alliance War) guild of a different faction, but that's more of a social aspect.
The only thing GUILD related is claming resources/keeps for the guild - you can't claim for this guild if your character does not belong to the guild faction. That is all.
It does not prevent you from joining with other faction chars. It does not limit your access to cyrodiil.
Guild membership does not grant cross faction grouping in cyrodiil.