Haven't used pkexec but after looking at it I'm not sure you need it.
We often run commands as other users from root's crontab by doing something like:
Code:
00 * * * * su - myuser -c "/path/to/myscript.pl" >> /var/log/myscript.prod 2>&1
This tells it to run the script called myscript.pl as the user, myuser, instead of as root.