The best part of this theory may be that it is short but it may bring some food for thought.
Let us assume for a moment that there are at least two timelines or perhaps at least two universes. Let's say that Jacob is in one alternate time/place and MIB is in the other. If it is impossible for someone from one time/place to kill another and MIB wanted to kill Jacob, then a loophole would need to be found. Could our mixed up Ben be that loophole? MIB said he had been waiting a long time for it.
Ben was trying to be a good person and do the right thing in his childhood despite his father. His being shot and taken to the temple destroyed his innocence. Going through the temple experience exposed him to the other time/place (the dark side?)and to some extent he had one foot in one world and another in the other. Perhaps this allowed him to kill people in both worlds.
I'm not sure if Ben could always differentiate between the two time/places-thinking Alex could not be killed, not being able to kill Widmore etc.
Just a couple of ideas.