I have taken a few spec ops missions (...) all of them have been to murder civilians for...reasons.
As I have written in some other similar thread: it's how modern wars are executed. Long time ago some strategists realized that killing enemy is less profitable than maiming him. Kill a soldier and your enemy will replace it with fresh one. Back to square one. Exhaustion war which leads nowhere.
But maim soldier and your enemy will have to take care of him. Yes, will have to. Otherwise civilians will start rioting against government. Who wants the leaders that don't care about their people? So from simple PR POV gov will take care of wounded soldiers. This way they will pour money, staff and resources into treatment of wounded, not into warfare directly. Costs will rise without providing war benefit.
Now - what it have in common with civilians. Well... strike at the soft place of your enemy (civilians) and sow fear among them. They will demand protection, they will put pressure onto gov. They will have to be dealt with. If gov neglect them, they will overthrow current rule and elect more keen one. In the end - it will destabilize your enemy. And this may help you achieve your goals.
Morally: despicable.
In terms of victory: viable.
Are there any "good guys" in the game. Don't get me wrong, I am an incredibly cynical human being but it would seem to be a little much (actually a lot) to have every faction engaged in such activities. Is this the case?
apart from above - you're missing one thing. White gloves operation and expendable assets.
We have a faction. Faction has it's own structure, resources and forces. Any moves from their side will attract attention. So they devised a "white glove" operation - let's hire a mercenary for the dirty work. It's that kind of mentality: "
we want them dead but we don't want it being tied to us. Ofc we profit from it but no one can prove it's us behind it. Not directly at least". So that faction hires a mercenary. Unaffiliated CMDR that for the right price will do anything.
Expendable asset.
You.
That way they get two ships at one shot. Achieve their goals. No direct connection. If accusations occur - "hey, that CMDR is not part of our ranks, we are not responsible for his actions. Admittedly regrettable actions but we cannot answer for that. True - we used services provided by that CMDR, it's a common practice to outsource certain task to independent pilots. In this case we treat it as terrorist action performed by independent and unaffiliated party."
Now - a subject to think about:
How do you know that next mission to assassinate clean "pirate" isn't a contract against previous "expendable asset" that has expired it's usage and has to be "dealt with"?