There are people who are just bored (mod did this, and no, they are not "bored", the real reason is far beyond that...) that get their jollies abusing and beating up on other people. They do it because they know it's hurtful to another living person (by definition, sadism), otherwise they would simply target NPCs. It has absolutely nothing to do with skill, they play with the specific goal to torment and cow other players.
Don't forget that sadism runs the gamut from emotional to physical abuse, and trolling for other non-combat willing/capable commanders to ram/abuse/kill is essentially emotional abuse, of a real person.
In an on-line game where you grief other players that don't wish to engage in combat, is real-world sadistic behavior, end of story.
Before idiotic comparisons to CoD or other obvious PvP games comes up, ED is absolutely not a PvP-centric game, it is a exploration and wealth-building/ranking game, with a minuscule legitimate PvP aspect. The NPCs may act like a threat in the game, but they are utterly insignificant in impact compared to a motivated griefer.
To combat the griefers, ED needs to have a much better way of distinguishing between players that have killed human commanders outside of "consensual" combat*, versus NPCs. Yes, it might be a tad immersion-breaking, but I'd have a murderer have a bright red box surrounding them, both in the scanner and forward-view, galaxy-wide, for at least two weeks.
You want to play with fire, fine, you pay the price, and then see how much fun you'd have with the huge jump in bounty hunters that would sign-up to hunt you down. (I'd do it in a heartbeat, if such a system existed)
I could honestly give a crap if you like shooting up "clean" NPCs, maybe they were part of a mission, not for me to say, but killing other players is an utterly and completely different thing, and the current "Wanted" status is useless in that regard.
This proposal will inevitably lead to whining about "But that's how I want to play the game...", but I hate to break it to you princess, but that not how the vast majority of others (your potential victims), want to play the game, so you'll need to suck it up if that's "The way you want to play..."
*Obviously CZs and other unique circumstances where one would obviously expect armed opposition would be exempted, but all other general open space would be a no-go for trolling. (maybe Anarchy space is OK, but the trolls would get really bored waiting for someone to pass though...)
Lastly, if you say you want to roleplay, and be a "pirate", that's fine in theory, but the game does not really support this profession in any viable way, both from an income side (extortion, meaningful cargo theft, etc), nor from a consequence side (oooh, you're "wanted" in that system for a murder...)