I completely agree. This is an underhanded way to kill Enterprise app distribution. We paid the $300 enterprise developer license expressly to be able to distribute custom apps this way. Our clients have very specific app requirements and do not want their custom apps on the App Store. Requirements change quickly and we were able to respond to their needs with very quick fixes and updates; going through Apple approval process would kill our response times. Their end users are not tech savvy and this new multi-step-digging-into-settings trust issue is a huge barrier to app adoption.
The "Untrusted" dialog does not even give instructions; even the most tech savvy users have to call tech support or google to figure out how to get the app to work. This needs to be resolved to allow a link off the the dialog to allow the app to run.