[Alt-text] Spongebob and Patrick work out their strategy with a utility based analysis.
We tend to assume that the means accomplish the ends, but that's not necessarily the case. The trolley problem never looks at where the trolley is going, just how it gets there. But if the way we want to get there doesn't actually go to the destination we want, then it's not a solution. Hope this helps. =D
edit: trolley is spelled with an e
I think the question "do the ends justify the means" is meant to invoke exactly what you're describing. What you call the "desired end state" is what the question means by "the end." The question is framing exactly what you're saying: the path of reaching a desired outcome includes everything it takes to get there--is it still a desirable end? Is the entire path justified, given the intermediate consequences?
I'm guessing it's worded this way because we apply this question/principle to situations where the "end" is altruistic but the "means" are not, and it's specifically asked because people want to separate the two to ignore the moral/ethical implications of the means. The entire point of the question/principle is that the end cannot be separated from the means with regard to whether it is ethical.
Maybe, I suspect we're just disagree on semantics without much meaningful difference, but I guess a simpler way of putting what I was saying is more "if you think that the "means" aren't justified by the "ends" when all is said and done, then you haven't actually achieved the "ends" at all, so if they would have been a good thing or not is now a moot point."
Let's say a goal is a description of properties of a world state you would like to achieve. A goal can then encompass many possible world states, where unconstrained variables can be anything.
So if you want A, that does not necessarily have bearing on B. So people might say that the ends (reaching A) don't justify the means (causing B). However, I'd say they underspecified their goal. Usually, people's goals are goal + all of ethics.