From Blizzard:
Guild affiliation with the Alliance or Horde will depend on the faction of the Guild Leader, and guild achievements and vendors will still reflect the guild's primary faction.
Guild members of the opposite faction will benefit from unlocked shared perks but cannot contribute to specific achievements. As an example, Alliance members of a Horde guild could not contribute progress towards the "Alliance Slayer" guild achievement.
Guild repairs and social conveniences, like shared chat, will be available to opposite-faction guild members.