Independent pirates who don't work for anyone but themselves are in every aspect an annoyance to the Rogues. They're nothing more but competitors who don't wish to work together with them, or be of any use for them at all. They use their piracy grounds, shoot/hunt them (over 50% of them in reality), and do use the Rogues' bases "for free".
While I must admit that I support the vanilla pirate groups like Lane Hackers (of which you rarely see indies), and dislike the terrorist-like Pirate ID which can be (ab)used by anyone. And it's sad to say, but there are only a few who actually RP with the Rogues, giving them a reason to have them docking on their bases.
Like it's often the case, the well-doing other half has to suffer of such changes. So they either have to use Rogue/Hacker/Junker/Freelancer IDs now.
Woah, you're going to chuck out the whole batch muffins because one or two of them are burnt?
When I'm on my Rogue and see indie pirates, I don't jump the gun and get straight to shooting them and vice versa. We help out each other.
Out of every single Pirate ID'd player I have seen, I have only ever seen one person attack Rogues without diplomacy of any kind.
Heck, as long as you're nice, you can even get the CGS to leave you alone or help you out.
One more thing, the general 'in-bed' relationship Rogues have with the Congress needs to change.
Remember Humboldt? That was technically a Rogue system a while ago, now the Congress technically owns it. They even removed the docking rights of my Rogue, after I had helped them defend it against those who'd wish to destroy it.
And the whole Altegra and Ciplian thing... eh. Junkers in Sirius are generally meant to be piggy backing house pirates, however, it seems that things are the other way around. Step out of line and bam, you can get FR5'd by over pirate factions through the Congress themselves. Ergo, Junkers have more power over the pirate factions themselves. By lore, this is wrong.