I have this theory that the Others got manipulated into following Jacob when they really should be following MIB. It would explain why MIB was "very disappointed" in all of them. Maybe MIB initially recruited Dogen, but Jacob got him to go traitor (maybe MIB lied and his son wasn't really saved or something). Maybe that's why MIB couldn't go in when Dogen was alive, being an agent of MIB maybe meant Dogen can kill MIB (ala Ben with Jacob). Maybe that's why Dogen sent Sayid to stab MIB, believing Sayid being an agent of MIB can kill MIB.
But then again, I can't see why MIB would force Dogen to stay away from his kid....after all MIB wants to go home too. So putting Dogen in that position wouldn't make sense. It actually makes more sense of Jacob doing that to Dogen, as Jacob seems to believe in the sacrifice for duty thing.