I think this kerfuffle does point at something that would be nice to have ratified in the HTML spec somewhere: the idea that content exists in different qualities and formats, and that when the user requests to download the content, she's presented with the different options possible. Content negotiation still only has one chosen format come down the pipe; a decision that the user probably hasn't made.
Right now, we're stuck with everybody doing something different in the page design to do something that's pretty important and fairly intrinsic to much of what happens on the web. And so users just default to the thing they know works everywhere, which is Save As... It's not surprising some of them are upset.
The only issue I can see with this is that there are security concerns with being able to override what is actually downloaded when Save As is used.