Personally, I rather look forward to a computer program winning the world chess championship. Humanity needs a lesson in humility.
Just because science so far has failed to explain something, such as consciousness, to say it follows that the facile, pathetic explanations which religion has produced somehow by default must win the argument is really quite ridiculous.
The trouble with conspiracies, even those that are to everybody's advantage in the long run, is that they are open to abuse. If manipulators really had the powers claimed, they could win the lottery every week. I prefer to point out that they could also win a Nobel Prize for discovering fundamental physical forces hitherto unknown to science.
I think that [Jay] Gould's separate compartments was a purely political ploy to win middle-of-the-road religious people to the science camp. But it's a very empty idea. There are plenty of places where religion does not keep off the scientific turf.