Eh, I think MIB is Smokey. I can live with him really just being a pillar of smoke that simply took the form of MIB, but given that Smokey's motivations seem completely inline with MIB and his experiences in this episode, I'm going with MIB was turned into the smoke monster.
As for who is good and evil, I still don't see Jacob as good. Good and evil are a matter of perspective, and I agree MIB is sympathetic. Some might see him as a murderer, and others might see him as doing what needs to be done to escape his unjust imprisonment.