With the current setup, cross faction guilds run into serious issues as some of the profession trainers are pulled from non-neutral sources, meaning a level 1 horde char joining an Alliance guild with full trainers will get one shotted by the Honor Hold NPCs who represent several of the professions.
Ideally, they should all be pulled directly from Dalaran, as all of Dalaran's profession NPCs are fully neutral.
Only issue with this fix is that the faction AHs likely are incapable of NOT being hostile to each other. Hence, the DBC override to set GM island as a Sanctuary with duels, which should prevent the Horde and Alliance AHs from trying to kill each other or any players from the other faction.
Incidentally, the portals should be set up to not overlap between factions, so that all 8 racial capitals can be accessed in one guild, same with Horde and Alliance AHs.