This is exactly the direction I wanted to see for this. Here are some of my thoughts on how to get the story away from religion at the end:
Any time a particle is forced to take a stance, that is it is forced to be something other than just a probability function, then that alters the particle and hence the system has changed and can not be measured the same again.
Now let's say that collectively all the matter and energy in our universe combined has a single wave function of it's own, as does say the combination of protons, neutrons, and electrons in a Helium atom, then one can also say that any measurement on that universe would also force it to take a stance and therefore irreversibly change that universe. The problem is that you would need something outside our universe to make a measurement of our universe.
What if our main character the physicist is working on slamming particles together at the new linear supercollider in Texas (so a few years in the future) and tries colliding two Thorium nuclei together forming an unstable element, #180, that on its own is heavy enough to form a black hole...a very small black hole, but a black hole none the less. A few experiments later and black holes are created in such a way as to warp time and space to another universe. The only problem is the black holes are extremely unstable and disintegrate after a few pico-seconds...just enough for the physicist to send a few short laser pulses through. When he remakes the black holes again he notices that a signal is sent back to him from the other universe as well as the black holes become larger and more stable and a steady stream of light pulses come flowing out. It turns out that in the time it took for him to create new black holes the other universe that he sent the laser into aged by about 100 billion years compared to the one or two months that went by in our universe, and during that time another civilization detected his signal and built an entire space station with futuristic technology to await another signal from the physicist universe.
Upon receiving the signals from the other universe a connection is made and both our universe and there's is suddenly and inextricably changed. Bad things begin to happen. The signal that starts coming through after several years of message exchanges between the two universes are distress signals. Of course at this time the entire Earth is in on what's been discovered but it is again up to our main character to solve how he changed the world...eventually, and I haven't thought out how yet, he discovers he created two evil Gods in the universe. It's about this same time that major disasters start to strike Earth as well and it is found that interaction with the other universe created the same effect in our universe as well.
The physicist solves how to end both Gods in both universes. The problem is that the solution is to end the existence of both. He does. Two new universes roughly the same are instantaneously created through a new big bang. These new universes do not have either good nor bad Gods.
The last scene is a shot of how even without a God of any sort the earth still evolved to roughly its previous state. Then we see our main character again, though this time he is not a physicist he is a carpenter. It is the year 15AD, he looks like Jesus.