Thought experiments of just this kind have led many philosophers to reject consequentialism as the primary determination of ethical action, as I'm sure you are aware. However, even a die-hard consequentialist would likely conclude that your would-be assassin's action was reprehensible and had no other moral value. Why? Because it only makes sense to talk about the consequences of an action having moral value (or not) if they could have been predicted at the time. Without predictability (though of course never rock solid), consequentialism would be useless as a moral compass. Therefore, unpredicted consequences are fortuitous, but it's not meaningful to call them 'moral'. Thus also we condemn someone who causes harm through carelessness, claiming that he could and should have foreseen the consequences; but we also leave room for pure accidents.

Notice, however, that this is quite different from saying that 'bad' intentions might have 'good' consequences. Suppose, for example, in my role as emperor of the world, that I command a law that all people have to do X. The police force charged with enforcement of this law might be corrupt and vicious to a man (and so might I), but if the law has good (and foreseeable) consequences then both the act of commanding it and the enforcing of it have a claim to be morally valuable. This might help us with your thoughts about colonialism.

Problems of consequences in ethics have been discussed many times on this site. Please click on 'ethics' to your left, and search for 'consequences'.