Any player or group of players has the freedom and power to earn the credits to purchase and roleplay a capital ship.
BUT
Any other player or group of players also has the freedom and power to object to the use of that capital ship and use whatever methods they wish to both object verbally to its use, and object to its use on the server through the violent actions of their characters.
If one person has the right to say all by themselves "I bought it so I get to use it" then a group of players has the equal right to say "No you don't". That is the price we all pay for being in a community.
I fail to see any logic or reason in that besides the obvious example of a gang of bullies picking on one kid on the playground because he's weaker. Why do they have that right? Because there are more of them? I think that that it is a really s***ty attitude, one that we should keep out of our community. There's no need to have it except to breed bullies. Do you really want that? I hope not.
As long as the independents roleplay properly then they should be treated no differently than faction members. Why? Because they're both playing the same role in the game. The only difference is that the independent's own backup fleet is imaginary. If the factions roleplay properly, than one of their battleships is no more authoritative than an independent's. Of course, that means that the same battleship belonging to the faction would have more power than an independent cruiser, simply because of the chain of command - not because the BS is a faction member.