"My point is that somewhere along the line it becomes more useful to put a stop to ongoing evil and suffering even if it means that bad guys have to be turned loose without punishment or other adverse consequences. The question is, where?"

Now that you have rephrased the question from a pie in the sky "can't we just all get along" wish to a question of policy. This question really is asked from time to time, for instance should we kill that murderer al-Sadr, or is he more valuable alive. Should we have let Saddam remain in power or not? Bush 41 yes, Bush 43 no. Should we have openned relations with China even if it meant working with Mao? Should we have negotiated with Hitler to stop the war earlier but let him remain in power? Should we have let Castro remain in power? Should we kill Ki Jong-il?

To me the answer depends on whether future military action is likely to achieve the desired outcome, or if cutting ones loses is the better course; and retributive justice is of small importance in either course.