/usr is maintained by the OS, and contains stuff that isn't required for boot but to round out the system.
/usr/local is where local modifications to the OS go, these can be site-wide (company wide) and can be hosted on NFS for example for network boots. User installed stuff belongs in /usr/home/<name>/*. Users shouldn't have root access to install stuff in /usr/local.
Side point: it really bothers me that on freebsd the ports system takes over /usr/local. I expect /usr/local to consist of things that I as admin have installed by hand, and nothing else.
You can change where packages are installed using some make.conf flags. You can then install the software anywhere you want. Your users will need to add the new path to their PATH and you'll need to set some flags in rc.conf to pick up the new rc.d path as well (so software installed through ports gets auto-started).
Then again, when you install ports you as the sysadmin are installing those by hand ...
/usr/local is where local modifications to the OS go, these can be site-wide (company wide) and can be hosted on NFS for example for network boots. User installed stuff belongs in /usr/home/<name>/*. Users shouldn't have root access to install stuff in /usr/local.