Yes.
Webmin->Webmin Users->username->Open the Available Webmin Modules section and click on the Custom Commands link (there is a checkbox and then the module name is clickable…click on the module name). There you can choose No for Can create and edit commands?
This is the same process for permissions on all modules, it is not specific to this module. All ACL configuration in Webmin works the same way.
However, note that Virtualmin users are sort of “locked” to prevent you from breaking necessary permissions or opening up unintended security holes. I know you’ve said this is a dedicated Webmin user, so this note probably doesn’t apply to you, but in case anybody is just now learning about ACLs in Webmin, I don’t want them to be confused when their Virtualmin users do not have this feature clearly visible.