David,
Diane is the expert but I can provide some general comments.
These are only my opinions and practices and might not relate to all coaches. First, like your experience I had to deal with a toilet that would not stop running. It was a Headhunter toilet. I learned the flush valve is a simple device and if it continues to run the problem might be as simple as a small bit of debris in the flush valve diaphragm weep hole.
If your coach does not have one, add a large diameter ball valve between the toilet and the water pump but after all other house water supply lines. In that way if the problem happens again you can shut off the valve which stops the toilet from running, but allows full use of all other devices that need water. If it does have one, have everyone in your family briefed on where it is and how and when to use it.
I never add water to the coach without monitoring it. EVER! My coach is equipped with an automatic system that I will never use because I don’t need the grief that comes with either running out of water because it did not function, or having water overflow. I don’t know how fresh water got into your holding tank except through the toilet (see paragraph 3 above). I never fill my water tank without dumping my holding tank. If your holding tank valve was open when the water was filling you would have wasted a lot of water, but not flooded the coach. I know if it is mechanical it is going to fail so I try to think of the consequences when failures occur and try to determine before things happen how I will deal with them or prevent them.