I'd like to think so too, but I do wonder just how much was understood about the nature of disease and infection. It was only in the 19th century that typhoid and similar diseases were understood to come from bad water.
I forget the details, but there was a pump in Soho that was infecting everyone in the area, but no one connected the pump water with the outbreaks. Then some chap whose name I should remember, drew a map of the area plotting incidents of illness. Only then was the pump identified as the cause.

Similarly with plagues and other horrors - it was the air and odours that were judged to be the cause - hence nosegays and sweet smelling herbs. Malaria means "bad air" and no one ever considered it had anything to do with mosquitoes and bad drainage.

So I doubt if Silbury water was kept clean for health reasons - they might have wanted it clean because it tasted better though.