Specials are displayed through a process similar to this:
Once identified as a special, the product id is added to the products_to_categories table such that it is associated with the specials category id that is defined in the admin control panel for configuration->specials...

My suggestion instead of hacking the specials code would be to see/use a notifier in the specials code that follows the addition of the product to the products_to_categories table (or perhaps just before to prevent further processing of it). To investigate the category and if it is in the category(ies) or meets other requirements, then to not add it to that table or to remove it from the table. (Depends on which notifier, what condition the data is in at the time, etc...)