As so many have noted, it seems pretty clear that the white/good and black/evil dichotomy can't be that simple. So I've been wondering how we can interpret Jacob and the MIB in a different paradigm.
I'm reminded of Alt Dogen in The Lighthouse: he mentions to Jack how difficult it is for a parent to watch his child under all this pressure and be unable to help. Maybe that's the root of the Jacob/MIB dichotomy? In other words, think of the Island forces as two parents: one is the stereotypical "helicopter parent", micromanaging his children's lives because he can't stand to see them get hurt. He wants the best for them but refuses to let them stand on their own, swooping in to "save" them whenever they're in danger. The other force takes a "hands-off" approach, believing that the kids need to find their own way if they're ever going to grow up and mature. He lets the kids make their own mistakes, lets them get hurt, because he believes it's the best way for them to grow up. The former force is royally pissed at the latter force because all he sees is his kids in pain.
The thing is, I can't figure out which Island force is which. Jacob micromanages the Losties' lives, manipulates them, and refuses to let them hurt themselves (that is, no suicides among the candidates). He might be seen as the "helicopter parent" here---he orders the "kids" imprisoned in order to protect them (see, for example, his orders to Dogen). Smokey then would be the other parent, the one who wants the kids free to make their own choices. Notice how he isolated Claire: ostensibly an evil action, but in the greater picture, he forced her to toughen up, to grow up. Her friends were so keen on protecting her, she never had to learn to defend herself, and Smokey put her in a situation where she had to grow up.
But remember how pissed off the MIB became when he discovered that Jacob had brought new people to Island, knowing they'd only get hurt? That's when Smokey swore to kill Jacob. He slaughtered the Others who refused to listen to him---essentially, he killed those who wanted to keep the Losties trapped in the Temple, who wanted to keep them away from his influence--and perhaps, his protection. He killed very few Losties; he killed Eko when Eko refused to repent. He killed the pilot, and as we saw with the Ajira flight, the pilot can automatically be in a position of authority after a plane crash. Had Seth Norris survived, Jack might never have been the leader, and even more people might have died. Maybe he wanted Jacob dead so that Jacob would stop tormenting "the kids"? Maybe he wants everyone to join him so that he can "protect" them from the world--by killing anyone who threatens them?
Flocke didn't hurt anyone at the Temple foot (other than those who attacked him). He just scolded them like an angry parent. When Flocke met Creepy Ghost Kid, CGK said the Monster "can't kill him". "Him" might refer to Dogen, to Widmore, etc. Whoever it is, it's someone that Flocke really, really wants to kill, and he's very angry at the rules that prevent him from doing just that. But maybe CGK wasn't saying "he" can't die---but rather, just that Flocke can't be the one to kill "him." The Losties have to do the deed---the Monster can't do it for them. Essentially, the Monster can't protect them, they have to protect themselves. An idea which really pisses off Smokey.
Basically, I've been wondering how we can interpret Smokey's and Jacob's actions without referring to "good" vs "evil", as I'm sure those terms are inapplicable. If we view them as two incredibly powerful forces with very different "parenting" styles, it shifts the picture a bit.