Could the short form of the command "/sc" (silentcontainer) be removed or toggleable in config since that's a command frequently used by staff chat and this plugin prevents people from running the command.

You can use Bukkit's commands.yml to resolve command conflicts.

aliases:
    sc:
    - "staffchat:staffchat $1-"

/e: Should also note that Bukkit's aliases system does not have the capacity to assign permissions to the aliases it creates. If you want to do that (i.e. to clean up tab completion for users) you can use PermissionsSetup to edit the alias's permissions on startup.