Believe it's Blasphemy by Douglas Preston. Remember reading it and plot sounds exactly like that in the question. Was a great read.
From the Amazon page -
Like Isabella, a giant superconducting supercollider particle accelerator, the thought-provoking new thriller from bestseller Preston (Tyrannosaur Canyon) takes a while to power up, but once it does, this baby roars. The ostensible goal of Isabella's creator, physicist Gregory North Hazelius, is to discover new forms of energy, but what he really wants is to talk to God. The project, located inside Red Mesa (a five-hundred-square-mile tableland on the Navajo Indian Reservation), is behind schedule, so presidential science adviser Stanton Lockwood hires ex-CIA man Wyman Ford to go to Red Mesa and find out what's causing the holdup. Meanwhile, a Navajo medicine man, a televangelist and a pastor who runs a failed mission on the reservation are gearing up to pull the plug on Isabella before she destroys the earth. Science has often tangled with religion in this genre, but Preston puts his own philosophical spin on the usual proceedings, and when he gets his irate villagers with their burning torches headed for the castle, the pages simply fly.
The synopsis from the Wikipedia page
Isabella, a powerful particle accelerator has been constructed in Red Mesa in the remote Arizona desert, the most expensive machine ever built by science. A team of scientists under the direction of a charismatic Nobel Laureate, Gregory North Hazelius, experience trouble, and the scientists seem to be covering it up. CIA agent Wyman Ford is tapped to go to Arizona in an undercover role and find out what’s really going on. He discovers the scientists have made a discovery that apparently not only demonstrates the existence of God, but communications with it reveal it to be far grander and deeper than anything found in the conventional religions.
When part of the discovery becomes known to a local fundamentalist pastor, he interprets it as a sign of the End times and by way of viral email recruits thousands of people from across the United States into "God's Army". They storm the machine, killing anyone in their way, and destroy the entire facility. They capture the scientists, gunning down two of them, and burn Hazelius at the stake.
In the end, it is revealed that Hazelius simulated the communications in an effort to create a new religion, one based on science and particularly the Scientific method and the search for truth. However, Hazelius himself admits to the simulation performing "beyond its specs." Comparisons are made between Hazelius and Hubbard in regards to Scientology.