Many pre-existing traditional guilds and more serious hardcoe PvP guilds would greatly appreciate the implementation of a feature that allows guilds to set themselves as 'Alliance War Exclusive' meaning that players that join that guild can only engage in the Alliance War under their guild tag. There simply would not be an option to fight under another guilds banner when entering Cyrodiil - with the possible exception of an established 'white list' of other guilds set by the primary guild. Obviously a player account would only be able to join one such guild at a time - but that's exactly the point.
Having the ability set as a condition of joining a guild that a player would be fighting under only that guilds banner in the Alliance War would resolve a major issues many established guilds have with the 5 guilds per account mechanics in ESO. That would allow members to be part of non-exclusive trade guilds, RP guilds, PvE oriented guilds with family members and real life friends, etc. not in their primary guild - but at the same time would preserve expectations of mutual support, working toward a common cause, and members abiding by clear and long developed guild charters and codes of conduct that many of us have worked hard to establish over many years for the Alliance War PvP aspects of ESO. The ambiguity of arguments over 'well this is the way we do it in X guild', trying to manually police what alliance war guilds members join or issues of players grabbing resources from one guild then using them while under other guilds banners in Cyrodiil would be eliminated or greatly reduced.
Many players coming to ESO are older gamers or simply more comfortable or aligned with traditional MMORPG guilds and do not embrace the recent social network norms - for us there's still a difference between real friends and facebook friends - just as we already belong to a community of guildmates and would like to have real choices about how we participate in ESO's guild system. I'm hoping the developers are open minded and apply the same ability to chose how players experience the game just as they've done with the recent changes to the starting experience and other player feedback.