Mother originally believed in Sol.

Campion Sturges reprogrammed her. She shows love for her creator, and treats his will as the will of God, something she believes in.

He took a shortcut. He didn't actually"successfully" reprogram her, because that's beyond the understanding of humans at the time. He did the beat he could, which was to give a believer access to their god.

He replaced her devotion to Sol with devotion to him/her creator. And as such, she became controllable. He could map her faith into something more controllable -- a logical system. For Atheists, they strive to be logical systems.

So to convert Mother from a Believer/Mithraic to an Atheist, he simply made her religion based around a Logical Figure, the atheist (or technocrat) Campion Sturges and his vision for humanity.

If you take this to a deeper level, how to you control humanity? What if the Trust had the ability to make a real Sol that he could control? Then he could get access to controlling the Believers/Mithraic.

What if the technocrats, in an effort to control humanity's perpetuity for religion, created a god for them? A god that the technocrats believed they could control? And that "god" was really just an advanced technology that was beyond the understanding of its believers?

Hence why they are called Believers -- it's a very atheistic way to term the religious without the establishment of religion. They don't think, reason, or know -- those are the terms of logic; they believe.