Now you're starting to sound hysterical.
Unless you think any random passenger should always be subject to being booted, without notice, from their preferred/prearranged seat because someone went up to a gate agent (or called customer service) and claimed a "religious need," it's unclear what you're even arguing.
He only got on the plane because they told him that. He clearly said that he wouldn't have flown had they not switched it. Therefore I don't see why that is considered wrong to insist on it. "Hold up the whole plane while they deplane"? Yes. Because the he only got on the plane based on what the gate agent told him. Once again you're sounding like you're nervous that people can take advantage and claim religious needs. Right now we are discussing a theoretical issue, and a story that happened. Once he was on the plane, why ant he insist on it.
I'm not arguing for a random person to decide that they don't want to sit next to the opposite gender, because over there you know that there is a 50% chance of it happening. But if the passenger went over to the gate agent before the flight, and said that the only way he is flying is if he sits next to a person of the same gender, and the gate agent confirms it (be creative and don't over think it, its hypothetical), why shouldn't it be in his rights to demand that?