I too question the rampant spread of communicable diseases from the tops of contaminated water bottles.
It's challenging sometimes on an airplane to pour from big bottle to little bottle without having them touch, but it's far from impossible. I've done it many times and I've had it done for me many times by FAs (who I must say, invariably have exceptional pouring skills in a cramped, moving environment).
As ACYYZ/SD has pointed out, if there's something you need, just ask one of the FAs. In this case, I'm sure one of them will be happy to execute a perfect pour for you.
Or if you want, switch things up and go sparkling. That way you get a nice, new, sealed can of Perrier in J or soda water in whY so you remain contaminent-free.