I can control which users can run su or gksu by, for example, including the line auth required pam_wheel.so deny group=nosu in /etc/pam.d – then members of group nosu won’t be able to use su or gksu --su-mode.
However, this won’t stop anyone from using pkexec (and it is futile to prohibit the use of su without prohibiting the use of pkexec, since apparently pkexec offers same functionality…). Is there any similar way to control who may and who may not use pkexec?