All that changes was that an allied guild could not join Factions while it was still allied.
A Faction guild can still join an alliance after it joins Factions.
A Faction guild that was allied before the publish hit, like mine, is still allied.
Originally, Faction guilds being in non-Faction alliances was.....I won't say a bug, but it was something they hadn't anticipated and didn't think of when they did the long-asked-for guild alliance system.
Now, they are leaving it in because it seems to have caused few, if any, problems, and because it allows Factioners to be part of life on their shards to a greater degree.
I, for one, argue that Factions benefits, like RP does, when it is embedded into life on a shard and not an isolated group.
Now, obviously, they do need to fix the new Faction blue healing in Felucca bug.....But that ain't the same as the alliance thing.
-Galen's player