Oh, you can, but you need to understand that you have so many toys, and face so much opposition their is a slipperly slope, you’ll struggle to resist one own excesses, be it an essentially invincible support sniper who can non lethally eliminate everyone, or rolling to an area in a tank, using artillery, predator style therm-optic camouflage, silence anti-material sniper rifles, sleep grenades, or use your own prosthetic arm as a UAV drone strike.
Or all of the above. Truth is, you can “ghost” most of it, whether that means murdering, sleeping or not touching a hair on their delicate heads of everyone you can totally do it, but the bait is hanging over you, like “Gee, your silencer just wore out, you could call in a new one, that’s not cheating is it? Maybe you could drop in that new sniper rifle you just researched that, or yunno, you could put on that magic suit you researched that lets you make it foggy, that’d sure be stealthy!”
What kinda ship are you running with? I stuck with the scarab long after better ships were available but hit a wall in the end game.