You could do a survey which plugins your employees need. There can be different needs, e.g. technical staff likely needs other plugins than employees that ar more involved in administrative tasks. Then you can install these plugins on the employee’s machines.

After that you need to rename or delete <install-directory>\updater\GUP.exe to prevent users from installing any other plugins. As long as your employees don’t have admin access to Notepad++'s install directory, they are not able to revert these changes.

The disadvantage is that your users neither will be able to update Notepad++ itself nor the installed plugins. This is something your ICT department has to do.