I think Jacob's mother makes it clear that anyone who enters the light will suffer a fate worse than death, and the constant mention of their inability to hurt one another was supposed to convey that when MIB was thrown into the light, he DIDN'T die, he suffered that fate worse than death: i.e., to become a sort of disembodied evil thing tied to the island (or the light beneath it) forever. MIB's body was probably just "shed" in the same way a way a butterfly would leave a cocoon. This wasn't just Jacob's origin story, it was the smoke monster's too.

I don't think the smoke monster existed before Jacob threw MIB into the light, I think it is MIB's light "going out," as their mother said it would if anyone tried to take the light.

That explains why MIB still thinks of the Mother as HIS Mother, and why he displays a familiarity with Jacob in later scenes, as well as why later seeing Jacob as a child would also have an impact on him.