User blog comment:The Milkman/Everybody Shut Up./@comment-2249774-20120526054202/@comment-4950455-20120526091330

"IT theorists claim that the "God Child" gives this option because if he didn't, Shepard would realize this was an illusion and that they were being indoctrinated. I'd say this is a sketchy reason, but entirely possible. "

I'm prepared to bet significant amounts of money the indoctrination theory is false, but I have to play devil's advocate on this one: there's actually a less sketchy explanation here if we take the position that the Catalyst scene is partially metaphorical. The Destroy option isn't being literally "offered" by the Catalyst/Reapers - instead, it represents Shepard's mind trying to break free of the indoctrination.