The Spanish Inquistion as much political as relgious.  As the video pointed out, it was really under the control of the Spanish crown rather than the Pope.  The routing ouf of crypto Jews was of political importance, since these falsely converted Jews could act as a 5th column and undermine its authority during its wars with Muslims and others.  Plus their present could undermine the genuine conversion of the fellow former Jews, and thus undermined national unity.  The crown percieved adherence to Catholicism as important to the national unity of the state, and viewed non Catholics as undermining that unity, and potentially weakening the crown, which is why it reacted the same way to heretics and Protestants.