Ok so here is my theory on why MIB is evil. So far everyone we have seen on the journey with MIB in the original timeline has had an evil side in the flash-sideways. With the exception of Claire, who we have only seen a glimpse of her FST.
Keep in mind the line Carmen Reyes said to Hurley in the episode The Lie, "A good man doesn't kill two men, a good man doesn't kill any men".
1.) Sayid - The first time seeing Sayid in his FST episode Sundown he appears to be a good guy, bringing flowers to Nadia, trying to help out his brother Omar, bringing their children gifts, walking them to the bus stop and even babysitting!! By the end of the episode though we see him revert back to his old ways by killing Keamy and crew.
2.) Sawyer - Even though he told Charlotte that he got to a point in his life where he was either going to be a criminal or a cop, obviously he has chosen to take the good side. But based on what he told Miles at the end of Recon, he still has that revengeful evil side in him. He is still hunting down Anthony Cooper and wants to kill him.
3.) Kate - Kate still seems to be on the hook for blowing up her old man. She is also still running from the FEDS. In What Kate Does, we see her helping out Claire. Claire being the same "crazy women" with MIB as her "friend" and his first appearent recruit while posing as Locke.
4.) Jin - While I am more hesitant to put Jin in with this group he is still on the Journey with Flocke. We haven't seen much of Jin in the FST, but the times we have seen him he still seems to be working for Mr. Paik as a henchmen, delivering the watch and whole lotta cash. At the end of Sundown we see him tied up in a back room, who finds him, none other than Sayid.
So far in the FST the people with the most interaction with each other are these four. Sawyer with Kate in the elevator at the airport and later running her down in Recon after she crashed into his car. Sayid with Jin at the restaurant. And keep in mind the line Keamy had in Sundown that he loves eggs. Eggs = Easter eggs, we know the writers love them too!!
We can also make the assumption with the group on Jacob's side, Jack, Hurley, Ben, Ilana, etc. as being good in there FST. Jack is not drinking, he has got a better relationship with his son now, he tries to help John Locke with his paralyses. Hurley is now a lucky "dude" and his lottery winnings seem to be doing good while not cursing him. Ben, in his FST has a better relationship with his father and is not the manipulator he is in the OT (well not as much). He thinks of his student Alex advancing in life before his own advancement.