Who's to say either even had an afterlife? The flash sideways was a construct of the Oceanic survivors to find each other when they died.
Jacob and the MIB were not ファン of each other. They had no reason to reconcile.
Also, with each having lived at least 2000 years, I think the last thing they wanted was an afterlife. Jacob especially was tired and very over it when he died, coming back as a ghost only to help defeat the smoke monster. He made it clear that once the 火災, 火 burnt out, he would be gone for good and forever. Makes sense.
The others had unfinished business with each other. All sorted によって the time we saw the church scene.
