Is it a SPS? If so, it won't be harmed by being exposed during the water change. I'd splash water on it to keep it moist during the WC process.
Some LPS corals could be damaged due to the weight of themselves hanging down while the water is lower. Elegance corals would be a good example of a coral that you should not expose during a WC.
>...Although I like to try to siphon some of the crud off the surface of the rock.
Siphon the crud while everything is running (your sump should handle this unless you are using a siphon too big), then do the WC from the sump as suggested above.