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ROS has been IMO absolutely doing great job in making installation of this large amount of packages as easy as possible. Usually when you're on an officially supported OS like Ubuntu (full list for Kinetic), there's no need for hacking installation steps at all. In case you had to, then it's most likely something was done in a wrong way during installation.

I have not yet attempted to completely uninstall and then re-install, but hopefully that won't be necessary.

I would definitely clean and re-install all ros by something like following (running these two commands will only take a few seconds aren't they? (running time is long though):

apt-get purge ros-kinetic*
apt-get install ros-kinetic-X  (whatever you need)

Just FYI, python-empy is depended by some core ROS packages on my Kinetic:

$ apt-cache rdepends python-empy
  python-empy
  Reverse Depends:
  python3-empy
  ros-lunar-catkin
  ros-kinetic-catkin
  python-ros-buildfarm-modules
  python-ros-buildfarm
  python-bloom
  catkin
  python-empy-doc
  python-bloom
$ lsb_release -a
No LSB modules are available.
Distributor ID: Ubuntu
Description:    Ubuntu 16.04.2 LTS
Release:        16.04
Codename:       xenial

I have not yet attempted to completely uninstall and then re-install, but hopefully that won't be necessary.

I would definitely clean and re-install all ros by something like following (running these two commands will only take a few seconds aren't they? (running time is long though):

apt-get purge ros-kinetic*
apt-get install ros-kinetic-X  (whatever you need)

Just FYI, python-empy is depended by some core ROS packages on my ~~Kinetic:~~Kinetic, meaning you don't even need to bother installing it explicitly:

$ apt-cache rdepends python-empy
  python-empy
  Reverse Depends:
  python3-empy
  ros-lunar-catkin
  ros-kinetic-catkin
  python-ros-buildfarm-modules
  python-ros-buildfarm
  python-bloom
  catkin
  python-empy-doc
  python-bloom
$ lsb_release -a
No LSB modules are available.
Distributor ID: Ubuntu
Description:    Ubuntu 16.04.2 LTS
Release:        16.04
Codename:       xenial

Only possible situation where you may have to manually do something specific to the issue raised in this thread is when you already have em installed on your computer. In that case uninstall it in advance if possible.