The explanantion that J gave is that the song is directed to the terrorists who flew into the Twin Towers, and it refers to their saying that they did it for God. In the song, J is saying that he doesn’t buy that. "Tell the truth, you’re kidding me." I can see that point, more or less. But to say that: "I know God" — as if He runs the local record store — is either very arrogant or just plain naive. Granted that you even believe in God, which I don’t, you can’t speak with any certainty about who He — or She — is, and what He does and does not want.
Apart from that, the question is not whether God — or Allah — would actually approve of killing thousands of people. The question is whether the terrorists believed they were doing it for God. "I know God, and that’s just crazy." Okay, it is crazy. But then, these terrorists were a bunch of insane fuckers — so why would you expect them to have a sensible justification for their actions?