Description of problem:
# package-cleanup --cleandupes
This command will remove the lower version for each pair of duplicates that it finds. When it removes the lower version, it can also remove dependencies of those packages. That happens when the dependency isn't a duplicate.

Version-Release number of selected component (if applicable):
   package-cleanup
   yum-utils


How reproducible:
   Everytime a duplicate package is a requirement of a non-duplicate package.

Steps to Reproduce:  
####This is just an example with NetworkManager. 
####It can happen with any packages that depend on each other.

1. # rpm -qa NetworkManager-libnm
        NetworkManager-libnm-1.0.0-14.git20150121.b4ea599c.el7.x86_64
2. # rpm -ivh --force --justdb NetworkManager-libnm-1.4.0-19.el7_3.x86_64.rpm 
3. # package-cleanup --dupes
      Loaded plugins: langpacks, product-id
      NetworkManager-libnm-1.4.0-19.el7_3.x86_64
      NetworkManager-libnm-1.0.0-14.git20150121.b4ea599c.el7.x86_64

4. # package-cleanup --cleandupes
  

Actual results:
Removing:
 NetworkManager-libnm   x86_64   1:1.0.0-14.git20150121.b4ea599c.el7    @anaconda/7.1   1.4 M
Removing for dependencies:
 NetworkManager         x86_64   1:1.0.0-14.git20150121.b4ea599c.el7    @anaconda/7.1   8.8 M
 NetworkManager-team    x86_64   1:1.0.0-14.git20150121.b4ea599c.el7    @anaconda/7.1    32 k
 NetworkManager-tui     x86_64   1:1.0.0-14.git20150121.b4ea599c.el7    @anaconda/7.1   258 k


Expected results:
package-cleanup verifies if it should remove the lower or the higher version duplicate. Potentially it would judge which version would cause the least amount of damage to the system. Verifying the files against both duplicates to see which package is actually installed.

Or if it could have a flag to affect only the rpm database, or ignore package dependencies.

Additional info:
cleandupes has no warnings to customers. Especially customers who have duplicates and GNOME installed, the issue becomes much much worst and removes majority of the system. 

The only thing that forces it to stop, is if it tries to remove yum.