I would say that Reverend Hale doesn't believe that Elizabeth is guilty of witchcraft. There are a number of reasons for this. First of all, it's telling that when he visits the Proctors, the main focus of his questioning is John, not Elizabeth. And in the little test he gives them, it's noticeable that it's John, not Elizabeth, who can't recite all of the Ten Commandments. (No prizes for guessing which one he forgets.)
Moreover, if Reverend Hale really were convinced that Elizabeth was a witch, then it's pretty certain that he wouldn't have simply gone to the Proctors' for an informal chat; he would have turned their place upside down looking for evidence of witchcraft. He would certainly have had both the power and the authority to do so.
Finally, when Ezekiel Cheever arrives with a warrant for Elizabeth's arrest in Act II, Hale is rather surprised. This doesn't seem like the natural reaction of a man who's convinced that Elizabeth is a witch.