Clearly, apps that cache data need to be modified to show the difference between having no data and having no data cached. IMAP clients have dealt with this, for example; they show a message like "the contents of this folder are not available offline".
Perhaps Apple could have made cache cleaning opt-in on a per-app basis until iOS 6, though.
The main issue is that iOS is deciding that you don't need something offline without asking you. I don't want my cached email to turn out to have been deleted because I downloaded something else entirely.
Many people would prefer the old method, where it would say you were out of space, and you would have to go free up some space.
Perhaps Apple could have made cache cleaning opt-in on a per-app basis until iOS 6, though.