I've been thinking about such a system but I will have to agree with Arne. It is the only drawback to constantly circulating the water. If the municipal system becomes contaminated then your stored water and the system become contaminated. Then you're really out of luck.

But being able to isolate the stored water and change it out with a few turns of some valves would be better.

I've gone through a couple of boil water orders. The problem isn't the boil water orders, but the delay between the order being issued and wide scale notification.
http://www.nctimes.com/news/local/article_7613d888-bc6c-5403-828b-df4e6086582f.html
You can expect anything hooked up to the water supply to be suspect.

If I was to setup a "buffer", I would set it up with two buffer tanks. One would be isolated and stagnant, and the other would have water flowing through it. In the event of water contamination, at least one tank would still be safe.
1) Switchable valve from municipal supply leading to two buffer tanks. The tanks would not be in use at the same time.
2) One way valve to each tank to prevent backflow in event of loss of municiple water pressure
3) Gravity fed valve (faucet) on bottome of each tank
4) Second one way valve on each tank leading from tank to house water circuit

Flip valve in line 1 to alternate tanks on a regular basis.

If your water supply goes out on a regular basis, this might be worth the cost. Otherwise stay with bottled water.