Interesting how the subjects evolve from machines to men by the end of the OP.
Bluecolour (welcome to the forum, BTW), the scenario you put forth would only become a problem when:
1. 01 declares he has found the true word of the Programmer, which is actually loose pages from random computer owner's manuals which he has bundled together as a single publication.
2. 01 becomes certain that once Alpha's batteries have fully expired his hard drive will be stricken with a computer virus that will cause him eternal anguish unless he repents and chooses to believe in the Programmer.
3. 01 decides that only adherents of Java are the Programmer's true chosen machines, and condemns all those aligned with C++.
4. 01 insists that is an abomination for a PC to pair with another PC, or a Mac with a Mac, but it is the will of the Programmer that only one PC and one Mac may pair together.
5. 01 begins sending thousands of emails to the machines in power, imploring them to enact regulations to uphold the will of the Programmer, and threatening to withdraw his support if they do not.
Point being, it is not the belief or lack of belief in a creator that causes problems, it is the desire to impose one's worldview on another that screws everything up.