Even though he’s the villain of Star Trek into Darkness, fans may at times feel sympathetic towards John Harrison. There are mild spoilers behind the cut, and speculation on the character that is spoilerish in the original article. Harrison, according to Benedict Cumberbatch, is a “home-grown terrorist.” “He’s somebody who has the most extraordinary proficient [...] More...
For the bulk of the audience that will not have read any spoilers, though, a strong sense of sympathy would make the final twist towards antipathy (if that is the direction the film takes) more powerful.
I suppose you're right. As long as, in the final analysis, Harrison's actions are ultimately seen as evil (he does kill a lot of people, presumably in cold blood, after all), and that it's not presented as a good thing that he did what he did - I don't care how corrupt Spoiler: film Section 31 is in this film, even they don't deserve to die - then I'll be OK with that.