I don't know yet how PolicyKit works, but this whole password dialog functionality seems wrong. The way I see it for desktop use, what you need is absolute control of the xserver over the local input.
This would solve for example the convenience securely enough when only one user has local access to the computer:
If you are in the high privilege group and want to execute some root command then press ctr+alt+del (invent a combination that only the kernel and xorg can read) and take absolute control on the cursor. Nothing but a local mouse can move the cursor. Show a dialog that says: "you are going to execute command_name. Click OK if you want to go on".
If an application wants to run as root, again, dialog "Please press ctrl+alt+del" to grab focus of click cancel, bla bla", then show the previous dialog where you click OK.