On the one hand, this episode of Star Trek makes fun of Christianity. Rodenbury gets a dig in at creationists by saying Landru has existed for 6 thousand years. The portrayal of BetaIII's inhabitants apes the stereotype non-Christians have of Christians that they just walk around blissfully happy with big smiles on their faces. The nature of the planet's inhabitants also eludes to atheists thinking religious people can't think for themselves.
On the other hand, this episode serves as a warning from Gene Rodenbury from back in 1967. It tells us what life under the new world order will be like once the mark of the beast is put in place. No one will have any will of their own. They will be controlled by computers through the microchips in their hands or foreheads, albeit it won't be a world of peace and tranquility by any stretch of the imagination.
The view that is outside this Landru versus atheism box is that of true Christianity. Yes, God has set laws for us to follow and He wants His will to be our will, but He also respects us as individuals. He created every one of us with our own unique personality, talents, likes, and dislikes. He wants His will to be our will so He can have us reach the full potential He intended for each one of us.