If you can't issolate new fish I wouldn't add the water to the tank.
Never know what you are fetching in, even good lfs have deseased tanks.
But this really isn't about the diseases. If the tanks are diseased, then it won't matter whether you add the water or not. The fish will still infect your tank as they will be the carriers. I guess my question is what problems can be introduced to the tank via the water only. In other words, if you went to the LFS and just got a quart of their water, just water, nothing else, and put it in your tank, what problems could it cause?