It's not unheard of to make alterations to the script during shooting. For example, on set improvisation or perhaps if an action sequence isn't working then it might be rewritten. Because of the strike though, they couldn't effectively change anything (though really, I wonder who enforces a thing like that) and had to shoot exactly what was written.
Really though, the best thing about the new film is now that they know how much we love lens flare, Abrams will include twice as much. We'll have to wear sun glasses to watch this movie.