"People have this unfortunate tendency to sympathize with the main character of a story, even if they're not a sympathetic character."

Exactly my point. That's why they should've made Jack a lot less sympathetic to make up for the problem you mentioned above. Maybe have the Meriff's reasons for turning on Jack being more sympathetic, you know. The Lost Legion kidnapped his wife (who was also 7 months pregnant), and threatened to kill her unless the Meriff cooperated, this being the reason why he sold out Jack to Zarpedon.

And instead of Jack letting him off, he doesn't care about the Meriff's reasons and screams at him about his betrayal. And instead of the Meriff shooting Jack when he turns around, Jack instead turns around as if he's going to let it go, then he jumps over the desk and strangles the Meriff to death, stating afterwards that it was exhilarating.

And again, when it came time to shoot the scientists out the airlock, Jack taunted Zarpedon over the ECHOnet that he was about to kill one of her moles, and Zarpedon replies that it doesn't matter to her, since none of them are actually working for her, but Jack kills them anyways. Later, you would find out (through ECHO logs) that those 4 scientists were completely loyal to Jack, and that the mole was the lady who was dumb enough to open the window on Helios and get herself sucked out into space. Jack, however, wouldn't care, still calling what he did "awesome."

And when he revealed the Eye of Helios, he would say that he was going to wipe Pandora clean of "bandits," but make it clear that he saw everyone on Pandora as a bandit, not distinguishing between bandits and civilians. Roland, Lilith, and Moxxi repeatedly try to correct him on this and make him realize that there are still a fair number of innocent people down on Pandora, but Jack refuses to listen, even cutting them off a couple of times. Eventually, Roland, Lilith, and Moxxi realize that Jack is too delusional to listen, and decide that he has to die, thereby triggering their attempt to destroy the Eye of Helios, and him with it.