Now, I can't speak for any other factions, but I can tell you that the XA has absolutely no problem with independants whatsoever. We don't consider ourselves to be the entire Xeno movement, so there's a lot of room for independants. We often fly alongside them and have a lot of fun in the process, and we treat them as equals.
As for needing to be in good with the leaders, that is definately not true. I didn't know anybody at all when I filled out my XA application. I flew a couple indie characters before that, but nothing major, and I didn't get on anyones radar, since I was still new to the server. When I was flying indie, I didn't feel stepped on by any factions, either.
Now, what the XA does do is try to lead by example. We always try to stay in character, and we always keep our loadouts in RP. Basically, if you want to know how to properly RP a Xeno, take a look at an XA player. Personally, I think this has worked, as I've noticed an improvement in the quality of indie Xenos since we came on the scene.