Just because you having heard of Freedom Corps fighting any of these other factions doesnt mean it hasnt happened. There is a lot on the hero side that hadnt been mentioned until COV came out. Take for example the Wyvern or the Legacy Chain. Not one mention in COH but they are fully fleshed out organizations helping to fight the evil forces in the Rogue Isles.
Something else that is bothering me about all of this is that just because it says the choice is permanent when it is made doesnt mean down the road you cant make ANOTHER choice!!!
I mean I really hope for more content past level 50 and who knows maybe then you can tell ALL the patrons to kiss your "you know what" and punk out Lord Recluse himself!! I really think everyone just needs to sit back and let the Devs play this one out because I believe we are just seeing the tip of the iceberg here.