Aren't we forgetting that God can do whatever he pleases? If he wants it to flood, it floods. But then, one must wonder why it was necessary for it to rain for 40 days when God could have twitched his nose like Samantha Stevens and produced a flood in about a nanosecond.
But I guess I'm forgetting that he wanted to kill everybody because he was angry. By letting it rain for 40 days, he made the death slower and more painful. God seems to delight in inflicting pain, doesn't he? Just ask the Amalekites.
Oh, wait, I forgot, God blotted out their memory, huh? But, gee, I sure seem to remember them from somewhere. Maybe God was just kidding. He's such a card.