I see how that could be trouble. A few things I'd like to highlight about the user name change situation:
1. Joomla 2.5 also allows for the user to change their name (if the option is enabled). This means both J 2.5 and J 3.2 allow this. Theoretically we could have the name change option depend completely upon the user setting in Joomla (admin section). This way we would not have to worry about anomalies of which admin has it enabled or disabled.
2. Community Builder is able to allow username changes, even if Joomla's config has username change disabled. Maybe not the wisest method, but it does exist.
3. When it comes to apps, it should be storing the user's ID instead of their user name. Right? Keep in mind, right now an admin can change a user's name. So if an app depends on the user's name to stay the same, your going to end up with the same problem down the road because admins are going to change some user names from time to time. With this in mind, it's very important that apps be able to work with user name changes. Otherwise why allow the admins to change a username in the backend ES users if it will mess with apps?