Installing Network Link Conditioner for All Users (Yosemite)
Ran into the exact same problem. Installed the Network Link Conditioner when my system had OSX Lion and XCode 4 or 5. Great tool but did not need it again until today. Found it no longer worked.
My system now has OSX Yosemite and XCode 6.4 so I downloaded Hardware IO Tools for Xcode 6.3.
Got the same message about not being able to replace it since it was installed together with OSX.

My solution was to first drag the tool from the opened .dmg onto the desktop and to then manually replace the tool using the command line:

cd Desktop
sudo mv /Library/PreferencePanes/Network\ Link\ Conditioner.prefPane Network\ Link\ Conditioner.prefPane.old
sudo cp -r Network\ Link\ Conditioner.prefPane /Library/PreferencePanes/