I've not kegged before (so probably not the best resource) but it would seem like you are going to over-carbonate if you can't relieve the pressure built up as it carbs naturally. I would probably take it off the gas now, relieve the pressure that is in there, wait for it to finish carbonating naturally, and put it back on the gas at serving pressure.
I know there is a safety pressure relief on kegs but is there a way to set one up to relieve pressure at a given setpoint to achieve the desired pressure to carbonate at during the natural carb?