I agree that you should catch what you drain in a clear container to see if there realy is water in it. The WIF sensors are well known to go bad and trigger a false warning. If you indeed find water,the best action is draining the tank. A diesel shop can seperate water from fuel making it good as new. Your plan of draining will surfice if you drain as soon as the alarm detects water. No,I would not drive 50 miles much less 200 after the indicator says water in fuel.
Do not use an additive unless it clearly says it is suitable for treating water in diesel. And then only if other options can't be used for some reason.
As far as Flying J,if you never had a problem before fueling there and it turns out to be water,they owe you for repair.