I have thought a lot about what the loophole is. I am referring of course to the loophole mentioned in the finale of Season 5, where the MIB mentions that he will eventually find a loophole.
The word 'eventually' really caught my attention, and I realized that the MIB (as Jacob's nemesis) would never stop until he found his loophole; his way to kill his rival.
As a result, the killing of Jacob was inevitable, and nothing could stop it, since the MIB had all the time in the world (it would seem) to find this loophole. From the very inception of the show, this would 'eventually' have to happen, and thus, the show could not end or even move into its final stages until Jacob was killed.
This got me thinking: the loophole for the MIB to be able to kill Jacob is that Jacob could only be killed in the end of the second to last season of the show, because they would need at least one more season to resolve the death of Jacob.