It may appear that UI designers are just working in ivory towers, pushing arbitrary and capricious changes down upon you. When you find yourself thinking that way, just think of the poor caveman.
"Treat people as if they were what they ought to be and you help them to become what they are capable of being." -- Johann Wolfgang von Goethe
That is the perfect antithesis to Microsoft, Apple, Google, Facebook, Twitter, the list goes on.
Also, with the new Versions stuff in Lion/Mountain Lion you don't have any extra data leakage. The latest file on disk (depends on the app I guess, but most naive apps that use Versions) will be just that, the latest, unlike Word where retrieving old versions/text is relatively simple and can cause an hotbed of issues...
Then I press Cmd-Z a few times and save again. It's really not so bad. And in this supposed glorious brave new world of auto-versioning, the old version is still available right? So even if I totally forgot it still wasn't "dangerous", at least any more than the new behavior is so.
Let me give one example - I sometimes want to read the content of the file (inside its own app), maybe make some changes and then Save As a new version. I do this mostly in MS Word (for Mac and thankfully they haven't gotten rid of Save As yet). We keep different version in different files, especially for our team. Updating the original file by default is simply stupid in my case.