I can not believe I am going to agree with ryokon, but you know what they say about the sun shining some times.
A character in a faction is in no way guaranteed to be a good RPer, what they do have though is a mediocre of accountability.
You can talk to their faction leader easily enough and discuss situation to find common ground.
This can be harder with indies but is still possible.
I like to think I treat every indy I come across as an individual and not just on the grounds of if he is in a faction.
His ingame rep, name and attitude are far greater indicators of if I am about to have troubles with him.
We can discuss this indy vs faction debate till we are blue in the face, but one thing I have come to learn is that people act as they choose and you will not change that.
If you are ignored by an official faction, the best thing you can do is ignore them back.
You don't need them to play and have fun.