If the situation is not clear than why include them in the franchise anyway. Doesn't make sense.
Their names were put in by IPL/BCCI. The government did not provide any clarification on their visas. The franchisees (all of whom are corporates) decided to minimize their risk and exposure to the Pak players since their status has not been confirmed by GOI.
Sohail Tanvir was one of the key players in Raj Royals triumph in IPL 1. They were still banking on Tanvir for IPL 2, but then 26/11 happened and the rest is history.
Franchisees would rather bid on a player that they are certain will play.