Historical examples? Are we counting self-defense or soldiers defending their homes? Or is that too pedestrian and not nearly grand enough?
Well, along the "grand" line of thinking, if I remember my Egyptian history correctly the reason their pantheon is so fracked up is that it's actually a melding of two (or more) pantheons. Way way back in time what happened was that, to unify the Nile, whoever it was that had influence (can't remember) managed to smash the conflicting pantheons of the various tribes. Now, I'd call that spiritual violence (manipulating religion for earthly gains?) and a pretty terrible means, but the end result (a unified Nile that would last hundreds of years) was a pretty shiny thing.
Now, if you like religious lines, then you have all sorts of wonderful examples... every sword-point conversion is a "ends justify the means" situation... provided the person holding the sword was right. Then there's Christ himself, who (depending on your favored history) was either a revolutionary bringing revelations or a lie concocted by the Romans to try and reign in the Jews. Either way, either he's saving some people by throwing the old followers to the wolves or it's all a lie to manipulate the masses.
Quick swerve to the East and we have the Black Ships forcing Japan to open their doors to the western world at cannon-point. I don't think it's a tough argument to say it's pretty terrible to point a gun at someone's head in the pursuit of money, but the result, that Japan became a first-rate player in the world, is arguably for the betterment of everyone. Of course, they did have that nasty civil war and fling with fascism along the way...
Sticking to the East for a bit but swinging more northerly, we have Russia. They're kind of Case A for doing terrible things in pursuit of supposedly noble intentions. But let's focus on Catherine the Great for a second. Depending on which scandalous versions you like, she basically usurped the throne, had the real king imprisoned, and then eventually had him offed out of spite. But she was *such* a better monarch then he was. Kinda morally questionable to have your hubby chained to a wall and stabbed, but the end result was actually pretty good.
For that matter, probably half of the interesting succession stories involve similar cases. You could probably make a good argument about good ends/bad deeds just based on the monarchies of Europe.
Switching tacks, let's play "what-if"... what-if, when Columbus landed, the natives killed him and his crew, burned the ships to the ground, and hid all the evidence? Think of how many of them would have been saved if Columbus's life had been cut so short. Would Spain have sent another vessel? Possibly... but quite possibly not. After all, they all had a pretty good idea that it could be done, but it was still risky enough that Columbus's voyage was kind of a big deal. If he had just fallen off the edge of the world the colonization of the Americas by Europe could have been pushed back by a century or more, and who knows what would have happened then? For that matter, if the Indians had just been unquestionably violent with the Europeans from the start they could have saved their civilizations from destruction. Would that have been a "good end" even if it meant slaughtering every pale-skinned person (bastard or saint) that landed on their shore?
Now, in any and all of what I've said, could a different choice had a "better" result? Oh, quite possibly. But the choosing between two unequal goods is a different question.
