A Proposal which hopefully should not require extensive changes and should mostly leverage existing code.
A way to issue a console command from a script; it could be a method of the Plugin class (or whatever you think appropriate) taking a string with the console command to execute (and possibly a Player object, as some console commands apply to the issuing player) and forwarding the command string to the console interpreter.
The goal is to support commands which are not possible (yet?) via the regular framework and, more in general, commands which could be automated to simplify the life of server owners/admins.
The implementation may be rather bare bones: just a boolean as return value (did/didn't get through), no error report, no particular validation, etc...; it may be already qualified as temporary and not supported in the future, etc...
It is a kind of a hack, I know, but it could save the day in some cases...