Well, lets face some harsh realities here: your other option is mostly a pipe dream, since there's simply no way that anyone was going to convince all of the warring empires to suddenly stop fighting and love each other. Ideally yes, that would be good, but when does that ever happen? Maybe I'm a pessimist, but I see violence as a fact of life--every day, probably every minute, peace is kept in the world because someone punches, threatens, arrests or shoots someone else. Even in the Book of Mormon (and I apologize to the non-Mormons for getting into some religious history here), the righteous warriors greatly outnumber the humble pacifists--just a few years after the Anti-Nephi-Lehis won a war by not fighting, Captain Moroni won a war by killing thousands of enemies and executing hundreds of traitors.
In that light, I saw the movie's message as impressively peaceful: sometimes you win a war by dying, the highest level of swordsmanship is to love your enemy, and the end goal of any soldier should be to put down his sword. Is there a level of evil justification in this? I think that's unavoidable--good ideas are always going to get warped by people who want an excuse for their bad ideas.
It's impossible for us to know what would have happened if historical events had gone differently--if Qin had preached peace instead of quelled dissidents, would enemy rulers have listened? If he had failed to unite China, would someone else have done so? Would the empires have spent the last two thousand years killing each other? Which scenario results in more death, and is that even a fair measure of which scenario is "better"? We simply can't answer these questions.
For me, the movie was about one thing: sometimes you have to die in order to help other people do what they need to do--in the surprisingly Christian words of Emperor Qin, Sky showed matchless love for Nameless because he chose to lay down his life for him. Sky and Snow choose to die (or at least fake it, as we later learn) in order to help Nameless get close to Qin. Broken Sword chose to die to teach Snow that peace was preferable to revenge. Nameless chose to die to help cement Qin's reputation and thereby allow him to garner the support he needed to conquer the other kingdoms. If you say that Qin could have spared Nameless and gone on to unite the kingdoms peacefully, I say that such a sign of weakness (as perceived by those who had not yet learned the lesson of peace) would have gotten him killed within the week by his own men.
Let me add an addendum here, just so I don't come off looking like a horrible person--in most situations, such as raising children, I try to use love--Dawn and I have made an effort recently to avoid punishments altogether, and to simply teach our kids why to be good rather than slam them for being bad. In a perfect world we could do that with everyone, from children to gang members to terrorists to tyrants; I simply don't believe that we live in a perfect world. Sometimes you have to fight for what you feel to be right.