Why does Hale want Danforth to pardon the people in prison?

This is basically because he realizes this whole witch hunt is a scam. Reverend Hale has become increasingly disillusioned at the obvious finger pointing and petty grievances that are done in the name of witchcraft. He is on to Rev. Parris's agenda and he knows that Abigail is a fake. Unfortunately, should Danforth pardon these innocent people, the whole travelling witch trial show would be out of a job. By Act 4 Hale quits the court.