I thought Batman's (in this example) logic was that unassailable boundaries are what separated him from the supervillains he fought. To kill one would mean he 'stooped to their level', and is no different: doing something he is not authorized in his legal power as a vigilante to do. That the justice system who handles these criminals are both sympathetic enough and inept enough to incarcerate and again lose them again is more in service of the story; if the Joker is a good villain, why kill him?

All for One being alive could be because we was not killed in the arrest. For all we know, he may be on death row. It's been only about a month since the battle. Trials can take months or years to set into motion, and he surely won't be killed while awaiting trial, unless someone took things into their own hands. Due process. You can argue that 'special circumstances' should skirt it (kill him now), but who makes that call, and is that person willing to take responsibility for the legal and criminal consequences? All Might had the best chance to kill him during their fight, but only could muster enough strength to incapacitate him, and the media was watching closely so none of the first responders had a chance to 'accident' him to death, which would have required pre-meditation to begin with.

Clearly the authorities feel confident in his incarceration (auto-guns, brainwave monitoring, ect), so there is no need to kill him if there is any possible usefulness to him being alive like information or the benefits of studying him.