This can be done using the "set-global-feature" command.
# virtualmin set-global-feature --disable-feature webalizer
And, if you ever find something that cannot be accomplished from the command line that is possible in the UI, it's probably a bug, and one that we'll address. You can file a ticket at Virtualmin.com for things like that. There are some things that aren't reasonable on the command line, like the system status graphs, but generally if it's something you could reasonably want to do from a script, we'd like to make it easy to do. I believe API coverage is very close to complete, but every once in a while new stuff comes up.
The usage for this command is:
Turns on or off some Virtualmin feature or plugin globally.
virtualmin set-global-feature --enable-feature name
And, I've noticed we haven't regenerated the documentation lately, so the man page for that command is missing from our online documentation. I'm working on that now.