Those clans defended scavengers from their faction, people they would have shot if they were in another faction.
Anyway, i don't see why you want to torn appart the server to appeal the most immature unable to adapt players, and kick out the newcomers and all who enjoyed the server. AOP doesn't have to be Fo2 clone. It is quite the opposite. People should be able to choose the server that suit them.
Anyway, i knew people from various clans, and none of them complained about the faction system (beside you). Many complains were about the lack of features in Phoenix, beside ZC/PVP/Scavenging, the lack of NPC "characters" in Phoenix, the lack of dungeons early on, the grinding related Power Armor when it came, the melee sneaks, the assignements done outside of Phoenix, the whiners that complained about noobs, the fact some dev were more busy making new guns instead of new important features, etc...
Some of these complains were adressed by the dev after some time, but some of the players had already left.
There was also some true noob/casual that never played Fonline or any MMO, that came in AOP thanks to the huge communication around the project and who considered even AOP as too hard for them. Considering most of the experimented players were also learning the rules of the servers, leveling their chacters and gathering items, we weren't enough available to welcome them and teach them, which i deeply regret and try to make up with current newcomers. Some others just left when the new shiny things came out (Wasteland 2, Divinity Original Sin, Dead State, etc...)
There are also the langage barrier. In Fogen, for instance, we are willing to translate the game in french, to attract french players who don't understand english, but i was said by a dev that it was too early to do it, that there will be many text changes in the upcoming months. Once there will be french, german and other translations, there will be a few more players.
But all complains/praises aside, let's not forget that AOP is in a beta phase, the very first open cession, and hopefully currently only have half the scopes it will ultimately have.