It's Cold War propaganda.

Literally "Animal Farm" in a single sentence.

Tropes can easily become cliches if done poorly, but in essence they're just common concepts in storytelling. The idea of having a protagonist struggling with finding what lines they won't cross, and accepting what consequences result, can make for a really compelling internal conflict. And having a no-kill rule is often a practical one for longer series in particular.

Imagine if Batman's rogue gallery couldn't be re-used unless the writers had them always be able to get away when their plans are foiled. When Batman instead sends them to jail, they can be shelved for a while without making Batman look very selectively incompetent at actually catching criminals. Instead, it's justified as a principle that he upholds, while giving the writer opportunities to also show character growth for villains. And if you argue he should focus on the greater good by permanently eliminating threats, then it can be viewed as a character flaw that gives him depth.

He’s interacted with the trolly, now he’s responsible for the one death and must be punished accordingly

It's the difference between defense and vengeance. In Transformers One they had already defeated the big bad and had the support of the other transformers, so killing him then was an unnecessary act of revenge. It's different when you're still fighting and the big bad's death could make a difference in the outcome.