1) Let's start with the fact that up until this episode Dr. Ben Linus was known as the leader of the 'Others' and the keeper of the Island from being revealed to the world. This was his job. We all knew him as very cunning, relentless man who was living on the Island in the village surrounded by the electo-magnetic fence, which we all saw at the beginning of season 2 (if i'm not mistaken) when the 'Others' saw the plane divided in 2 pieces and crash, then Ben sent some of his men to infiltrate the survivors. THAT was his life before the crash.
So, back to our Episode 7, in which we see Ben's life, had the plane never crashed the Island, i would expect to see our Ben in that village working those birth issues that Juliet was brought to solve, or to see whatever daily life he had THERE.
But what in the name of God is he doing outside the Island, teaching in school?
2) Let's proceed with why does Alex refer to Ben as Dr. Linus instead of 'father'?
And why does Alex give such a worm treat to Ben, when we all remember how she hated him in the first seasons, right after the plane crash.
3) Last, but not least, in our Episode 7, Ben is giving up his dream of becoming a school principal, in favor of some recommendation letter for Alex, when we all know well that he was a self utilitarian person from day 1, and we all remember how he even sacrificed his daughter to save his ass when those mafia guys, sent by Charles Widmore, came to kill him. Now, ok he was sorry for this later and so on.. but that doesn't change the fact that during the entire show Ben had always and consistently took care of his own skin, in the first place.
4) In addition, when we saw the future lives of our survivors, had the plane never crashed the Island, THOSE characters did stay within the script. Shepard stayed the good old spinal surgeon, Kate stayed the same outlaw we knew earlier, Hurley still that same lottery winner, and the list goes on.. only Ben Linus for some reason had to become some school teacher and so incoherent.
In my personal conclusion, i find this episode to be very inconsistent with the real history of Ben in this series, and inconsistent with his own character behavior as well.