I don't think you realise that the Southern Alliance calls itself that because it is meant to operate in Texas, California and New York, leaving Colorado to the Northern Navy. Since there is no Northern Navy counterpart right now (and probably never will be), the SA want to get rid of this pointless limitation of their ZoI and just be the established Liberty Navy, so they finally can in their RP patrol Colorado. Why does this immediately mean they will kill all indies is beyond me, and I cannot see your reason at all.