You know, we just MIGHT be something similar to a simulation. We may even not have free will in the truest sense, in that a simulation can only run random action generation to a specified degree. Bottom line, however, is that the universe is finite and we can’t know anything emperically about what is outside that finite boundary.
The question is: does it matter? Does it matter if we’re just a “programming” God’s simulation running inside of His “computer”? No, not really. Faith is still the same either way.
Second: does it matter if there is free will or not? No. Orson Scott Card goes into this subject nicely: whether or not there is free will, we have to ASSUME and ACT like there is, otherwise society ceases to function as we can no longer hold the guilty at blame for their actions, nor can we praise the heroic for their deeds. If there is no will, there is no responsibility, and so society ONLY moves along on the assumption that we have free will.
In other words, the show is speculating. They have no way of scientifically knowing anything of the sort, and the idea that we don’t have free will is fanciful, but entirely useless in human existance… so don’t worry about their program because ultimately it doesn’t change a darned thing.