Keep in mind, I'm relatively new here, but even in my short time here I've seen things getting noticeably more hostile.
The biggest problem that I've seen is that some independents act as though even a simple request is a gross infringement upon a basic right of their existence.
Going to use LSF for my example, but this should apply to pretty much all factions.
I think there's room for non-faction LSF characters so long as they act like LSF agents and respect =LSF='s authority. I can think of quite a few reasons not to join =LSF= - some people seem to dislike the faction as a whole, perhaps someone might have a personal conflict with a member, and maybe they simply don't know if they'll stay interested in the character long enough to justify joining the faction.
As far as people using excessive force when "enforcing the law" when faction players aren't around, I think there should be an expansion on the posts about the laws of Sirius, adding proper procedures for enforcing the laws, so these independents actually have some guidance on how to do the job right. Short of in-game support, which is very unreliable, they don't have much help with knowing how to handle things. Since the police factions that exist already seem to have an established procedure for dealing with criminals, it should be a simple matter to describe that in a readily-accessible pinned topic for independents.