@Pluto this can be resolved by limiting guild member number, not allowing guilds to have infinite amount of members, but limiting to 150-200 max.
Sure alliances can be formed, but alliances are about politics, and are very fragile. And when it comes to PvP guilds, each guild will want "stuff" for themselves, and not to share. At least true PvP guilds who are most dangerous will.
I'm a member of PvP gaming community that plays through many years through several MMOs, and we were always "our guild vs the world", rejecting alliances and just accepting a challenge.
Just let guilds have some valuable rewards that can only belong to a single guild, and can't be shared with alliances, and this will prevent large alliances being formed as there will be no point in them. As spoils will only be able to go to one guild. And then having guild limited to 150-200 people max, you will always have battle among many guilds in the world, and will avoid one alliance being able to control everything.