Or DID he embarrass Pakistanis by acting as a hero, a role that Pakistanis revile?
Just about all the "offences" you cite are either phony or Dr. A. had no role in perpetrating. Dr. A. did not commit treason against Pakistan. He did not work with polio vaccines (and if you google search you'll find just who originated this idea). His Hepatitis A vaccine program was real. And so on.
Perhaps the real reason Dr. A.'s release is controversial is this: he may not want to leave Pakistan.
it never occurred to me that someone might want to stay in Pakistan