Are you saying it's very hard to implement a checkbox to disable WebGL? A lot of browsers protect you from opening or resizing windows via Javascript. How could disabling WebGL be more complicated? My browser is even warning me when a Javascript is running slow.
I mostly agree, but there's a bit more to it than that. For example, you want to be able to report back to the page that WebGL is disabled, so that whatever content is supposed to be there can degrade semi-gracefully.