The popup blocker is configured in Registry. It can be set up via group policy, registry editing and clicking through IE menus. There are no relevant startup parameters documented. Registry settings are divided to computer and user contexts; the former doesn't need special permissions. A group policy doesn't require special permissions from the user.
The last resort is to use a tool like Autoit to simulate clicking through IE menus. It is the most error prone a way, and I'd avoid it as far as possible.