Just because Anakin evidently ultimately fulfilled the prophecy to bring balance to the Force, I do not believe that that means that what he did in terms of falling to the dark side was right. I do not believe that any aspect of the narrative excuses Anakin's behavior merely because of the ultimate outcome
I entirely agree. Years ago I had a debate with someone about whether or not Anakin was "The Greatest Jedi Ever" and I disagreed,
wholeheartedly, precisely because of what you say - the positive end result does not excuse the means by which Anakin achieved it.
In other words, for me anyway, I can say that Anakin did his "job" (fulfilled his purpose) - but he didn't do it in a way I could excuse. If, by saying, "do your job," you also mean "do your job the right way from the start" (like Luke, more or less) then yeah, you could say that Anakin didn't do his "job" (which is why I said earlier that this seems more about semantics, rather than what actually took place).
Bottom line: by framing the Saga as "Anakin's story," Lucas is showing us that the ends do not justify the means. Of course, that only works if one buys into the stories the PT is trying to tell (the way Anakin is portrayed as falling from innocence into evil) - and given the many flaws of the PT, that's by no means taken for granted.