I asked myself the same when I was still an Indy. It felt like there was a huge division between the "real" players and the "newbie indians". It motivated me to get into a faction as soon as I could and - gladly - I was offered the chance.
I think it is fine for player factions to use the indies as a "pool" to recruit their members from.
I'd also say that this can only work satisfactory for both sides involved, when aid is offered to those not yet up to joining a faction (e.g. because of rule issues like ships, ID problems, IFF stuff or other newbie issues).
So it's a faction's job to help the indies. And not treat them as second class. And many factions I know try hard. Perhaps... just ask someone of the faction you'd like to be in directly. It might get you where you want to get.