I really think that there should be an option to prevent the CNR client from running as root. I am a stickler for security and control and really do not want applications running as root unless I specify.

The CNR Client does not actually run as root. It starts as root, but immediately drops privilages down to the user that started the client. For nearly all of the client's operation in runs as a normal user application. It is only when it needs to do something where it must be root like running dpkg -i <package> that it elevates it's privilages. And of course once the root action is done it removes privilages again. Although it is not as safe as a user application this is much safer than an application that really runs as root.