Look at the shipping modules ...
You will see that there is a function that controls them via the $this->enabled example on the file:
/includes/modules/shipping/item.php
// disable only when entire cart is free shipping
if (zen_get_shipping_enabled($this->code)) {
$this->enabled = ((MODULE_SHIPPING_ITEM_STATUS == 'True') ? true : false);
}
If you did a search in the Tools ... Developer's Tool Kit ... in the bottom input box for:
function zen_get_shipping_enabled
Select Catalog/Admin ... Click Search ...
You would find two files with this function ...
The one in the Admin just returns true so that the module loads properly in the Modules ... Shipping ...
The one in the Catalog checks for various conditions and returns true or false when the shipping module should be displayed ...
If you were to write a function to manage the $this->enabled for the storepickup.php to look up the customer's group_id then you could make a similar function to enable/disable the shipping module ...