The actual benefit of using ctrl-S (or cmd-S for us Mac folk) is that autosave is still not ubiquitous, and I'd much rather press cmd-S regularly when it's not necessary than fail to press it and then discover that I needed it. The great thing is that it's basically instantaneous now so it costs nothing to press it every few words, which definitely wasn't the case when I acquired the reflex in the late 80s or early 90s.

For this particular default I see no problem in overriding it. I'm sure there's only a minority that routinely uses ctrl-S to save a lot, but essentially nobody uses ctrl-S to save a web page that contains a document they're in the middle of editing, given how esoteric that is and how unlikely it is to produce a useful result.

That's not to say that overriding defaults is good in general. But there's no need to be consistent about it. Overriding ctrl-S is totally different from overriding the arrow keys, for example.