Systemd does indeed handle the shutdown, reboot and other commands, and the default privileges assigned are permissive. To change this, you need to create a Polkit rule. Create a .pkla file in /etc/polkit-1/localauthority/50-local.d (say, confirm-shutdown.pkla) containing:
[Confirm shutdown]
Identity=unix-user:*
Action=org.freedesktop.login1.*
ResultActive=auth_admin_keep
The various shutdown, reboot, etc. commands are, in Polkit terms, actions in org.freedesktop.login1, for example, org.freedesktop.login1.power-off, org.freedesktop.login1.reboot, etc. The specific problem here is the default configuration, which is in /usr/share/polkit-1/actions/org.freedesktop.login1.policy:
<action id="org.freedesktop.login1.power-off">
<description>Power off the system</description>
...
<defaults>
<allow_any>auth_admin_keep</allow_any>
<allow_inactive>auth_admin_keep</allow_inactive>
<allow_active>yes</allow_active>
</defaults>
Note that it allows the active user to power off, reboot, etc.