Copper, while perhaps permissible in some locations, is not ideal for natural gas. Sulfur in the gas, depending upon its concentration, can degrade the copper. There are approved flexible gas lines that can be used to supply appliances that may need flexibility, but normally not a water heater. When the pipe is kinked there is a larger risk of leaks and having gas enter the home.
You should think about replacement with black-steel, threaded pipe. You may need to call a licensed plumber, because the steel pipe may need to be cut and threaded to fit – beyond just buying assorted nipples and fittings at the hardware store.
If the gas company needs to come into your house for any reason – such as for a reported gas leak, to relight pilots after an outage, or a meter change-out, they will do a cursory inspection and lock out your gas service until it is corrected and re-inspected. Fix it all now.