I know the post is quite old now, however I've a solution that works with qmake version 3.0 (and XCode 6.2):
you should set the bundle name to the full path of your framework e.g
QMAKE_FRAMEWORK_BUNDLE_NAME = $$PWD/Release/yourframeworkname
note that the .framework extension is automatically added.
When linked to the framework, an application will look for it at this full path location.
macdeployqt could be used later to distribute your application.