Its never been said MIB can't hurt Jacob, just that there are rules/reasons that prevent them killing each other. It would appear that MIB found his loophole buy getting Ben to kill jacob for him. Rolling Jacob in the fire didn't really do anything more (Ben had done the damage), it was just a dramatic flourish that MIB really enjoyed.
There's a theory that God's only exist because people believe in them. Perhaps Ben stabbing Jacob was not so much about using a knife but more about Ben's loss of faith in Jacob and that is what "kills" Jacob.
From a scripting point of view, the Lost creators have been at pains to try let viewers know if someones really dead (eg Locke being hung). Rolling Jacob into the fire let us know that he definitely isn't going to recover from his stab wounds.