Oh man, that is seriously broken. I save-as in Preview all the time when cropping or color-adjusting photos, and this could've produced a very bad day if I had upgraded to Mountain Lion and kept doing that, unwittingly overwriting all my originals. (I haven't upgraded yet, partly to let things like this be come to light before I dive in.)
It doesn't overwrite all your originals because files are versioned in Mountain Lion. If you accidentally save changes to your original that you don't want, you can just revert to a previous version.
I used to do what you describe--open the original, make changes, then Save As. Until I accidentally hit Save instead of Save As. Goodbye original.
Now when I want to work off an original I make a copy of it first in the filesystem, then open the copy with the application (Photoshop usually). Since I never open the original with the app, I can't screw it up. I don't have Mountain Lion yet but the "Duplicate" functionality sounds like it will work for me.
In Mountain Lion, you don't need to accidentally save changes to original.. it automatically does when you hit Save As (which shows up when holding the Option key). And that is where this becomes bloody annoying. It means every time I do a Save As, I have to revert the "original" file to its "original version". That's idiotic.
