Basically it all comes down to how you RP, If your indie RP's well, like Gafwmn for example, the factions will leave you alone, and in many cases ask for your help.
If you ack like a twerp and bring shame to the faction's name then expect to be treated like a twerp.
if you are a decent RPer you shouldnt have to worry about disgracing the faction your indie represents because that would be OoRP. And on a different note, if someone is continually being a twit in their capship, or any ship, I see no problem with the faction they claim to represent PvP whoring them till they act right. This isnt a place for people to come and act dumb, its an RP server so RP.