Violence. Where there is no commonly agreed upon means of determining the truth value of a statement the only recourse is to violence. Thats why when religious people disagree they have 500 years of bloody warfare. When scientists or rational philosophers disagree they do an experiment or have a debate, or both. They all agree that logic and empiricism (the scientific method) are the highest standards of truth, so they have a means of resolving conflict.
Well, it depends. Just because I consider both effectiveness and morality important aspects of the debate, it doesn't mean I consider them equally or exclusively. I also don't view them absolutely; I'd compare them to the alternatives suggested - war or the complete dissemination of the nation ideology.
Well if you apply the Socratic method you could argue both positions independently, I just don't think it is a very productive thing to do. Firstly the argument from effect has been the mainstay of (classical) liberal debate for a good couple of centuries, and it has never worked. People don't fundamentally care that there will be more good stuff in the world because they are only concerned with what is moral.
So if one were to argue the case from effect, then, aside from getting caught in a web of statistics and debate over the validity of said statistics, one would eventually have to discard the argument and change to the argument from morality. But by this point it's too late, because in the eyes of your opponent you've already accepted the moral validity of the actions in so far as you are willing to debate their efficacy in the first place.
So my position is that you can argue from effect, and by all means do so. But be aware that you're not debating skilled logicians and that what you say first will influence their capacity to understand what you say later.
Finally, innocence and guilt are rather subjective terms.
They shouldn't be subjective in this debate; Because if you have already established as your premise that the government is guilty, then you must refer to the individuals doing business as the government. Their victims (even their military to a large degree) are acting under a coerced situation.
In terms of what one might call black-letter ethics; if a gunman points a gun at you and says "kill that person over there or you'll die," most people would agree that the only guilty party is the gunman. That is; there is no such thing as morality where your actions are coerced. And the degree of the coercion represents the degree to which actions of an individual are amoral.