Actually, the crayon in the brain caused the genius - Homer lost it when the crayon was removed.
Nope, other way around. Homer pushed a bunch of crayons up his nose when he was six and sneezed out all but one. Homer has it removed when he is working as a human guinea pig at a lab. Moe returns the crayon to Homer's brain at the end of the episode when Homer can no longer stand being a genius in a dumb-man's world.
If the situation were to have been explored in greater detail, I think Flanders response might actually have been "This looks right, but it can't be true. Still, I better not let this out." Then he burns the paper.
There was plenty of time for the detail you suggest, instead, Flanders calls the proof "airtight."
Homer: Hey, Flanders, heading for church? Well, I thought I
could save you a little time.
Ned: Oooh, found a new shortcut.
Homer: Better. I was working on a flat tax proposal and I
accidentally proved there's no God. [shows Flanders a
sheet of paper with complex figuring on it]
Ned: [flustered] We'll just see about that. [reads the paper]
Uh-oh. Well, maybe he made a mistake. [checks it again]
Nope, it's airtight. Can't let this little doozy get out.
[uses a lighter to burn the "proof"]
[in the background, Homer puts more copies of his no-God
paper on the windshields of nearby cars]
on-line script
I think his Christian faith in itself would convince him that the "proof" couldn't be correct.
Bottom line - I can't hold that this little incident makes Flanders a hypocrite.
I think it is a defining moment for his character. He does it while he is alone, and importantly, doesn't speak directly to God about it as he does with so many other things in his life - such as the time he yells "God, it's me Ned!" after knocking over nine bowling pins (with the tenth following his plea).
He didn't respond to the proof with his faith as you "think" he should; he responded by attempting to hide the proof from the rest of the world.
This is the moment Flanders' faith is shown to be superficial.
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