Since we know that MIB could not directly kill Jacob, Flocke was used to trick an old friend, Ben, in stabbing Jacob to death inside the Tawaret foot. However, when Bram's men went inside the chamber, they tried to kill MIB but failed. The bullets bounced off Flocke, who then went around the corner, turned into Smokey, and killed four men. The question is why could Jacob be killed by a metal knife while MIB/Flocke could not be killed by a spray of metal bullets?
Here are possible variables:
1. Jacob was killed at night, and MIB attempted assassination took place at night. This could mean that Jacob was the ruler during the day and MIB at night. Each is only open to attack/death during the opposite part of the day: Jacob at night, MIB during the day.
2. Jacob was in a "human" form, with a body and blood. MIB was in the form of Flocke, which was a mere shape-shifting reproduction of Locke, whose body laid outside in the sand. However, when Smokey took Rousseau's crew through the temple wall, we saw the remains of the men. When Rousseau confronted the crew and her husband on the beach, she killed them with rifle bullets (in the day light hours). If one was consistent with the events shown, even though MIB forms replicated bodies of humans, those forms can be destroyed during the daylight by conventional arms.
3. Is the place of confrontation important? Jacob died at night inside a sacred structure. But MIB's form Flocke was also inside the same structure. MIB's other human forms were killed outside on a beach. With the Temple Others spreading gray ash around the grounds could be evidence that MIB's destructive powers can be used within sacred places.
4. When Jacob was stabbed to death, and he admitted that "he died one hour ago" to Hurley, Jacob turned into a ghost. Was this because he was killed and/or because his body was cremated? We have seen evidence in the past that the inhabitants were paranoid about having dead bodies lying around the island. Are dead human bodies the needed vessels for Island spirits such as Jacob and MIB? Well, MIB creates his human forms without inhabiting their bodies (example Locke). We are not sure about Jacob - - - that is why some have speculated that Jacob now possesses the long-dead Sayid.
Then there was the 180 shift of power at the end of the season premiere. When Flocke returned from the statue into the daylight of the beach, Richard Alpert saw Flocke in a totally different light, like a "mask" or veil of identity had been lifted: Alpert was going to say "is that you?" when Flocke greeted him with the "glad to see you without your chains" reference before beating him up. But the really odd piece of that exchange was the fact that Richard clearly shouted out to the Others not to fire their weapons at Flocke. Why not? He just killed Jacob. Was he worried about collateral damage? Probably not, as Bram's crew in the chamber were not hit by their own bullets. No, Richard's outburst was to stop anyone from killing Flocke!
Flocke used Richard as a punching bag to return to island alpha dog status. "I am extremely disappointed in all of you!" Flocke said as he started to march back into the jungle with Richard as his prisoner. Why was MIB-Flocke angry at the Others? Was it because they did not recognize him? Or that they did not recognize him earlier? Or that they did not have the guts to challenge him at that moment?
Other theorists speculate that in the black-white, night-day context of the characters, MIB appears to be the dark lord of this saga. The evil one who plotted to kill Jacob, the apparent Island ruler of the Others. Yet, there is a concept of a vengeful good god, too. One who is upset with his followers for taking the "wrong" path or taking direction of evil sins or not worshipping their true god properly. So it is still a 50-50 proposition on who is good and who is evil.