Hmm. When I'm done with an app, I usually hit the home key. I usually use 'back' when I'm taken to another app by some other means: an email notification, a link starting the browser, opening a file in a file browser. Perhaps the confusion lies in different usage behaviours?
And FWIW, I just tried doing what you describe with the ICS clock / alarm app. It worked as expected for me: after tapping "set", the alarm was set, and Back took me back to the clock, and another Back exited the app.
One practical way the new semi-broken approach affects me is with JustPictures, a photo viewing app. I use it in conjunction with ES File Explorer. It used to be that when you launched a photo from the file explorer, it would come up in JustPictures, and then you'd return to the file browser when you tapped Back. But now, after JustPictures was updated to better conform with guidelines a month or two back, it goes into its own "tile" view of the folder before sending me back to the file browser. This behaviour is according to the new guidelines, but I find it quite upsetting. I launched JustPictures not because it has its own top screen and file system navigation etc., but because it has more reasonable photo viewing functionality (specifically, file-based rather than media library based) than the gallery app.
The new Android approach seems focused on becoming more like iOS, where each app is its own silo, rather than how it started out, with activities blurring the distinction between apps and enabling a higher level of integration. But the more Android becomes like iOS, the less reason I have to prefer it over iOS.
There's actually a similar dynamic going on with Firefox. Firefox is slowly cloning Chrome's look and feel, and I have to work harder and harder to get the menu bar, status bar etc. back in place. The day I can no longer do that, is the day in which I might as well give up on Firefox and use Chrome. (Well, that and Chrome's text selection algorithm. It's absolutely hideous for this compulsive text-highlighting reader.)