Not so. If the wall works, then being a rationalist will allow you to correctly interpret the evidence of that fact, while irrationality might cause you to ignore the evidence and incorrectly conclude that the wall has no effect.
A better wish might be “I wish to believe that this wall grants wishes.” If the wish is granted, then you will believe truth; and if it is not granted, then you will also believe truth.
Excellent story.
The one thing that felt really out of place to me, literarily, was the passage “You couldn’t blame them, could you...? Yes, actually, you could.”
In a story about Hard Choices, it seems to me that the narrator shouldn’t tell the reader what to feel. It would be better to put these sentiments in the mouths of characters, perhaps the Kiritsugu for the reply, and leave the reader to choose who, if either, they agreed with.