One of the themes that connects the two parts of the movie is the idea that life is a field of infinite potentiality, and that when we as humans make a choice within that potentiality, we not only “choose” a reality, but we – in a sense --help to create reality as well.
The quantum physics part of the movie was all about how quantum mechanics is a physics of potentiality, of probability; and how the act of observing a set of quantum probabilities leads to one of those probabilities being “concretized”. A crude example would be to say that a box may or may not contain a live cat; once you open the box, then one choice among the many possibilities is given concrete form.
The more psychological part of the movie was focused on the idea that we humans are “addicted” to various harmful emotions: hatred, greed, anger, lust, etc.; and that we have the power within ourselves to release those addictions. The release occurs via choosing a beneficial path amongst the many potential choices.
I wouldn’t say that the movie is anti-organized religion. Instead it stresses the ideas that life, existence, the universe, is ultimately a mystery, and that joy is found in the questioning, not the answering. Various organized religions might find that idea threatening, naturally.