That one's been around for 28 years, and was finally fixed in Lion and Mountain Lion.
The "Save As" command has always been dangerous and ridiculous in the way it's typically used for editing and then saving duplicates. Lion finally gives you better and more safer options, but if you're not willing to learn what those are and how it works, if you're hell bent on continuting to do it the old way, then you're not going to like it and you're going to continue to risk data loss like you have for the last 30 years.
I, for one, love the way it works. Yes, I had to sligtly change my workflow but it's change absolutely for the better.