Leave the baffle in place, like blumby said, remove the blade disk and use a small pry bar to bend it downwards working your way around the perimeter. eventually you'll get it so it doesn't rub.
Oh, and yes there bodies have a tendency to flex a bit but when they do you'll find a blade rubbing on the deck, especially if there's a kink anywhere around it. It's a bit abnormal for the baffle to rub when the body is flexing because that is where the motor is anchored to the body and is therefore fairly rigid. Is it possible that a couple of your engine mounting bolts are loose?
