From General Order 2:

OPEN FACTION

In worlds where the KGB does not have an OFFICIAL FACTION presence, your affiliation with other organizations must remain anonymous and not be in conflict with KGB (for instance, you are a member of the XXX organization in a game called Kill Everyone Online, and the KGB is a foe of XXX in another world). If KGB leadership determines there is a conflict of interest, then you would be asked to either leave the other organization, or renounce your KGB citizenship. In worlds that KGB has or had an OFFICIAL FACTION or had a presence, the (GM10) High King / High Queen or (GM5) King / Queen may declare a OFFICIAL FACTION to be OPEN. This releases KGB citizens from the normal requirements of General Order 2 in that game / server, even though there is a KGB presence in that territory. This means that a KGB citizen may be a member of another guild in that region that has been declared OPEN, subject to the following restrictions:

You may never intentionally attack or assist in any nonconsensual attack against any citizen of KGB or KGB Organization at any time.
You may never use KGB resources (Web, Voice Communications, etc) against the KGB or any KGB member at any time. Such actions will be considered treason and dealt with per the KGB constitution.
KGB members that have affiliations with other organizations would be barred from holding any leadership position within KGB and could advance only to the rank of Knight. You must forfeit any leadership achieved at the time you join another organization. At any time, you may decide to give up those affiliations and become eligible for leadership and military advancement.



A similiar instance happened In Elder Scrolls online, although it was never intentional- it was just one megaserver that a few others decided to play a different faction on than most of us did, but we ended up bumping into each on opposing sides in the PVP part of the game, which lead to us to end up calling for a closed faction. HOWEVER, guilds work alot differently in ESO, guilds are crossfaction and you can be in up to 5 guilds at once, so we called for a closed faction so we could all at least be under one tag and coordinate where we were pvp'ing essentially, and so we couldn't hinder each others objectives.

My advise would be to nip this in the bud quickly before feeling get hurt.