Mine were bent like that and I just used a body hammer to tap them back into place. You can use a large steel or brass punch to get it up against the roof so you don't slip off.
Then, run a bead of high quality RTV windshield adhesive (the kind that comes in a big caulking tube) along the flat places....the whole length. Take a jack with a piece of wood and jam the brace tight against the roof (place it in the center of the rail) and let it cure. Do both rails, obviously. This will eliminate the loud popping in the wind, and still be flexible enough to not come un-done. The tube of adhesive cost around $15 but it will hold just fine as it's designed to hold in a large piece of glass.
Hope this helps!
Mikey