Well, they explain that the changes aren't caused by the butterfly effect, like other time travel movies, but by a time boom. The time equivalent of a sonic boom.
I agree that the reveal at the end is pretty cheap. The setup/payoff structure doesn't work if you get to the end and get the payoff, but never saw the actual setup.
And there's no way that Batman with a pistol could kill someone who can travel at the speed of light. (This was even worse in the comic, where Batman stabbed him with a giant sword)
But at the end of the day, Flashpoint is still one of the best DC animated films, because most of the animated films just aren't very good.