Hi, the red and blue factions/alignments used to be for battlefield entry. Teams used to be red vs blue only, however this feature was removed quite awhile ago to allow more equal matchmaking, so that more battlefields can start if there's enough people (no matter how many red or blue queue for it) and so those that are guildless can also join.
So at the moment it doesn't matter which colour you pick. If it ever becomes a relevant feature again, you also get the chance to change the alignment of the guild once if you need to ^^