1. Killing them hurts my rep with the independents. This is nonsensical. The independents are, by definition, an unaffiliated, misc. category of peoples. Why would they all care if I blow some random scavenger fleet? Also, they were going to kill me for the scavenge too! Why am I a bad guy for defending my own business and livelihood but when they do the same thing is "lawful."
I think the issue here lies more with the base game than anything, in how it handles Indies and your rep with them. I feel like people (and the game itself) forget their lore blurb:
"
Not a unified faction as such, the Independents are a loose category of polities and free agents unified more by a lack of association with a major faction than any shared qualities. Independent worlds and the spacers who call them home often share data, trade generously among themselves, and will readily cooperate to perform short-term security and military actions to better protect what freedom they have maintained by working together. Equally likely, trust can break down, and Independents will suspiciously deny each other favors, compete viciously, and turn a blind eye to the misfortune of neighbours."
So while they do hold those "loose" bonds, that doesn't mean that they should function as a hive mind that keeps track of every single thing that happens to every single random individual claiming to be "independent". They even outright work against each other, as per the lore, on many occasions.
But this feels more like a limitation of how reputation functions in game, more than anything. How it realistically should function, is that if you're doing a lot of black market trades on a certain indie station, picking off their salvagers in the system, etc, that base should develop a negative opinion of you. But if you're on the other side of the sector, fighting scavengers over a debris field that you created, defending that claim absolutely should not have any correlation to what indies elsewhere think of you, at all.
But again, that would require the rep system to function on a much more specific basis, sort of like how you have rep with officers you might run into. If something like that could be applied to individual stations/planets, and then the station/planet's rep then applied to their affiliated officers and fleets, Independents would feel much more immersive, and not like just any other faction in the game (which is exactly how they function, outside of immediately hostilities from identified combat).
The way I work with it is just using the console to relations to try to emulate that behavior, and then placing limitations upon myself at times in not being chummy with indie stations that realistically wouldn't like me. It isn't really a fix, but it's something.