The way the system appears to work is your account can be a member of multiple guilds but you can only be tagged with one at a time. You can change this on the fly, although the exact mechanic is not known.
I personally think this is a horrible idea. Guild pride means something. I am a Council Member of
What I propose is that guild leaders be given the option of joining Alliances with other guilds. Where if two guild leaders discuss it, they can together both go and form and alliance. As they see fit they can invite other guilds into the alliance, and when it comes time for raiding, or whenever the members see fit they can tag UP to the alliance, and tag back down to their guild.
This way guilds keep their guild pride, and strong alliances are formed allowing for an even greater in-game community. When WvWvW starts, guilds can tag up to alliance, and use their alliance to take over the same objectives that guilds can.