When we were down in Sept, they were enforcing this rule. My husband just waited until we had left the "dock" and were moving out of sight. Then he whipped off his shoes and threw them in the bin. He put them on quickly before we came back up to the "dock," while we were still out of sight. No CM was the wiser (and besides, they can't retrieve you once you are free floating...).
I just jammed my shoes (still on my feet) as close to the center of the raft as possible, way up under the bin. My feet stayed nice and dry, and didn't have to stress about getting my shoes on and off!
Never occured to us to bring flipflops (mine are leather anyway!), but this sounds like a good idea as well, if you don't mine carrying them.
Have fun.
Beatnik