Human thought is by default compartmentalized for the same good reason warships are compartmentalized: it limits the spread of damage.

A decade or thereabouts ago, I read a book called Darwin's Black Box, whose thesis was that while gradual evolution could work for macroscopic features of organisms, it could not explain biochemistry, because the intricate molecular machinery of life did not have viable intermediate stages. The author is a professional biochemist, and it shows; he's really done his homework, and he describes many specific cases in great detail and carefully sets out his reasons for claiming gradual evolution could not have worked.

Oh, and I was able to demolish every one of his arguments in five minutes of armchair thought.

How did that happen? How does a professional put so much into such carefully constructed arguments that end up being so flimsy a layman can trivially demolish them? Well I didn't know anything else about the guy until I ran a Google search just now, but it confirms what I found, and most Less Wrong readers will find, to be the obvious explanation.

If he had only done what most scientists in his position do, and said "I have faith in God," and kept that compartmentalized from his work, he would have avoided a gross professional error.

Of course that particular error could have been avoided by being an atheist, but that is not a general solution, because we are not infallible. We are going to end up taking on some mistaken ideas; that's part of life. You cite the Singularity as your primary example, and it is a good one, for it is a mistaken idea, and one that is immensely harmful if not compartmentalized. But really, it seems unlikely there is a single human being of significant intellect who does not hold at least one bad idea that would cause damage if taken seriously.

We should think long and hard before we throw away safety mechanisms, and compartmentalization is one of the most important ones.