chiming in a bit late, but you could always abuse /ex to execute commands and you can flag scripts on your server to only run when a flag is given;
if you're using Denizen as an example, you can use something like this:
debugging_command:
type: command
name: debugging
usage: /debugging
description: Enables Debuggy Denizen scripts
script:
- if !<context.args.is_empty>:
- narrate "<&[warning]>Just use /debugging!"
- stop
- if <server.has_flag[behr.developmental.debugging]>:
- flag server behr.developmental.debugging:!
- narrate "<&c>Debugging disabled!"
- else:
- flag server behr.developmental.debugging
- narrate "<&a>Debugging enabled!"
followed by adding a check for if <server.has_flag[behr.developmental.debugging]> to determine if it should run, or not. this includes while your server is live