I'm open to that possibility, but I'm not yet convinced, for a few reasons:
1. It just smacks of cheap irony. It's just too easy to say, "see, we'll make it seem like they're evil, but they're REALLY GOOD!
2. Hurley.
3. Flocke's offer to Sayid was straight out of the New Testament: Fall down and worship me and all of these things will be yours."
4. While I'm not going to go so far as to say that Jacob was good or has acted good, and certainly I wouldn't say his followers have, there seems to be a clear moral distinction between Jacob and his behavior towards both his followers and his enemies, and Smokey. Jacob has never acted in a wrathful or violent way, has never sought revenge, and has put people into a position to make decisions (albeit often manipulated by Jacob) for themselves. Smokey has repeatedly killed, threatened, directly coerced, lied, etc.
5. Look who is now on Flocke's team: Con-artist-murderer Sawyer, torturer-murderer Sayid, thief-murderer Kate, crazy woman murderer Claire, mob go-between Jin.
6. Look who's on Jacob's team: Doctor Jack, all around decent guy Hurley, mother/nurturer Sun, unknown quantities Lapidas and Miles, and multiple murderer Ben. Plus the members of team jacob that came on the plane, plus, by all appearances, Richard. Now, I may be missing something. I didn't watch the show religiously for a good chunk of its run, by I don't recall any of these characters intentionally killing someone, except for Ben, maybe Richard, and the plane people. But of the core characters, the candidates, none have blood on their hands.
Now, the teams may change up over the course of the coming episodes, and I think it's highly likely that Kate and Jin will switch teams. But when you look at the moral quality of these two groups of people, is it really hard to pick which are the bad guys?