I dunno man, I know/get what you're saying, but the way I kinda took it was this. I don't think he was thinking the ends justify the means. At least not after Zod.
This was a true origin story for Snyder's Superman. He learns who he was/is, realizes his powers, and for the most part just saved people because of his good nature. He wasn't Supermanning it, no flight, no suits, etc. He just went around helping people (seemingly) at random and would leave and disappear with no reward, no hovering in front of crowds, etc. He was willing to give his life if needed (the whole oil rig scene).
Then his first real threat shows up. (Several) Military Kryptonians that are just as strong or stronger and more experienced as he is, and they can pretty much each kick his ass. It gets to the point where Zod is gonna do what HE feels will justify his actions and murder an entire innocent planet, just so he could rebuild it in his own image. Clark snaps his neck because he knows Zod will never stop.
But then he realizes what he's done. Immediate regret and remorse. Maybe from that point, he decides that the No-Kill rule is needed.
Sure that's a stretch, I can admit. But I dont know what it is, Cavill's Clark/Superman was great. I think he was a perfect casting for the character. Zimmers score was amazing. Yes it's not Williams' theme, but Zimmers is amazing (check out the live version on youtube, it's ridic).
Could it have been lighter in tone? Sure. Brighter in color? DEFinitely. But I mean, we basically got what we wanted for years. Superman punching stuff and fighting another superpowered enemy, and not just putting out fires with ice breath, and catching Lois falling off a building.