Augeas looks nice, but a relatively mechanism-free way of doing this for .debs (the mechanism used could still be Augeas) would be to add support for configuration file updater scripts. Such a script could process a configuration file automatically and return success if it were able to complete the job without making any "unsafe" changes, and failure with an explanatory message otherwise. All messages from a dpkg configuration run could be displayed at the end of that run to avoid interrupting running updates. And packages like upstart, for which other packages are likely to provide configuration files, could export an updater script for use by those packages.
Of course, knowing the Debian packaging system there is probably already a way to do this now.