Generally, the official factions are quite good.
Unfortunately, trying to control a horde of people who aren't in your faction is no easy feat, demonstrated countless times on both sides of this conflict.
However there is some element of OOC dislike between the factions at this point, probably due to misconceptions that were never resolved.
I asked the colonials and miners to simply dock to avoid conflict on my 101st about a month ago, I was pleasantly suprised when they complied. They came back out afterwards and it lead to a good half a hour of RP before we went out seporate ways.
I've tried to do the same since and it never worked out, however that one time I'll remember:)
these are just symptoms. the real malady is lack of communication, and that comes about from one-sided groups. joining the CR? make an indy oc, and vice versa. if you see the fight is one sided, log into the other char and balance the numbers. epic battles are cool. epic ganks are not.