I mean that part of humanity is freedom, and part of freedom is the ability to choose, no matter whether that choice is the right one or the one that benefits you the most, much like your Matrix examples.

However, while I might agree with the fact that Graham Hess has the ability to choose, the lives of those around him seem to be predefined to lead him to that conclusion. Honestly, if I were in the same situation he was in at the end of the movie, I believe that I would be madder at God than ever because not only did God allow his wife to die, but he ordained it, along with the dismal life given to his brother and the illness given to his child. Then again, it did prove to him that God existed and intervened, and apparently a manipulative God is better than an uncaring or nonexistant God in his mind.

So, while I can see that Graham Hess is given a choice, especially since I would have made the opposite choice (or maybe the choice was to believe again, regardless of attitude), his family and the vet were not given choices. They were manipulated for a particular outcome.