That's the reason for the bypass circuit, to isolate the tank if necessary. Of course to be effective that means you must have some forewarning the tap water may become undrinkable. Some risk there, but last winter there was a freak snow storm in my area and we did get just such a warning, and believe me a large reserve tank would have been a huge help. Maybe it would be better to leave it isolated at all times, and only draw through it periodically as a refresher.
I would definitely say to leave it isolated, and rotate the supply occasionally.
In Pittsburgh, the water pipes were 50 years old, if we were lucky, and would burst at the drop of a hat.
When one of those pipes went, the entire water supply was immediately contaminated.
You have a fantastic idea with having your storage in-line for easy purging, but you must remember that in the event of a disaster, water lines will immediately become contaminated, so the name of the game is to have a water supply that will not become contaminated.
That being said, one of the best water storage options every one of us has is our hot water heaters.
You should also remember toilets, and if anything happens, run to your bathroom and fill up your sinks and bath tub.
You may have to boil the water, but it will be a huge supply ready for your use.
Also, an anti-siphon valve may be something you want to look into (if you don't already have one).
These prevent water in your house from back-flowing into the main water lines, so if something does happen, you will at least have the water that is still in your pipes.
One of the best sites I have come across for water storage, and other emergency preparedness topics is ProvidentLiving.org.
It is run by The Church of Jesus Christ of Latter Day Saints.
Yes, it is a church site, but there is a lot of good information there.
Water storage:
http://providentliving.org/content/display/0,11666,7534-1-4065-1,00.html