Had they not betrayed their deal with Khan and shot him, maybe he wouldn't have turned on them like that once he had control of the ship. "This is a new universe. Things are supposed to be different." is how its been put by fans of the film. The same logic applies.
We can continue to grasp at straws with the gigantic plotholes, or we can agree that the film wasn't perfect just like every other Star Trek film out there. Its like when the community was trying to figure out why old klingons aren't like new klingons. You can come up with all the wild stories trying to explain it all you want, but the truth is it was some decision made during the writing/make-up/production stages that resulted in an inconsistency.