This issue actually has a long and troubled history, going back to the dawn of the alliance system. (Which will never stop being a "new system" to me, just as barbed and horned and spined leather will always be the "new leathers.")
At first, due to a bug, Faction and non-Faction guilds were allied to ally.
Among roleplayers such as myself, there was some rejoicing, as it allowed Factioners to become more embedded into life on the shard, especially in Trammel. Guilds could participate in the advantages of the Alliance System in Trammel, could war guilds, etc., and also participate in Factions.
Though this was unintended and technically a bug, the devs made a conscious decision to leave it in....As long as it wasn't used as an advantage in Faction PvP!
Lots of fun was had among Roleplayers in Trammel. Some nice RPed, Trammel PvP fights occurred that otherwise would've had a harder time occurring. Spontaneous RP events and PvM hunts could be handled more easily.
Well, lo and behold, these alliances were over the years increasingly used as an advantage in Faction PvP. (Imagine that!) Primarily the issue was fields and area effects.
The difficulties were increasingly obvious as Faction participation increased during and as a result of the Warriors of Destiny event cycle, and other Faction changes such as the Faction Artifacts.
At some point, a funny thing happened.
Faction guilds and non-Faction guilds became unable to ally. However, previously-held alliances remained in effect.
At first, Draconi referred to the lack of ability to form new such alliances as a bug, saying it'd be fixed. Then he shut up about the issue for a month or two, until finally the official policy became that the alliances themselves were a bug, and it would be fixed (meaning that the existing alliances would be broken by EA).
And, eventually, this is what happened.
I don't like that such alliances can no longer occur. I understand it though. People will use it as an unfair advantage. The fact that people would do this hurts people who would use such alliances fairly and honestly.
-Galen's player
)