What's the Plus side for God in this story?

I was working on a study for my 5-8th grade bible study group today...We are going to be going over the Great Controversy. Now in my opinion it is hard to argue the rift between Good and Evil, God and Satan. It is hard to argue the existence of Satan. (I won't go into my challenges with using Isaiah 14, and Eze. 28 as proofs of Satan's rebellion) Anyways the belief statement ties the flood into this story and it got me thinking, how was the flood a win situation for God in the Great Controversy theme? Seems to me that the flood could have been used as proof that God was a tyrant that just wanted to get his own way?

Now I'm a believer in miracles and even in God's intervention in nature. But could the narrative about the flood be God trying to save people from an upcoming natural disaster, wanting to save everybody?

I'm not going to bring any of this up with the kids, but I'd love to hear some feedback.  How does the flood make God look good? Or how does it play into the Great Controversy theme? Isn't it just like the kid who is losing at checkers so they decide to knock over the board to get a new game?

Sorry to sound sacrilegious.
Benji