I don't think that Reverend Hale really believes Elizabeth to be a witch. I think that he feels that the Proctor household is "soft" on religion. Yet, I think that he feels that this softness could be misread by those in the position of power. It is for this reason that he is insistent that the Proctors recognize the changing tide of social perception and political power in Salem. He does not perceive Elizabeth to be practicing witchchraft. Yet, he also understands that the lack of religion in the Proctor home can be misread by many. It is in this light that Hale leaves with a type of proto- warning that they must find a way to be more demonstrative about their religious faith. I think that it is a statement on the condition of life in Salem that Hale would have to ensure that the Proctors are "church folk" in order to rule out the possibility of Elizabeth being a witch. The larger implication of this is that issues of guilt and innocence in Salem are being decided by public perception and shades of insinuation as opposed to issues related to actual evidence and a sense of institutional control. In many ways, Hale becomes a part of this.
When Hale visits the Proctors in Act Two, he has come of his own accord to get a sense of what the Proctors are like and how deep their religious commitment runs. It is important to remember that he is an outsider and has only heard innuendos and accusations about various Salem residents; he is an intellectual and wants to conduct a sort of independent study. After all, people's lives are at stake.
Though he is troubled by her absences from church, Hale accepts Elizabeth's explanation that she has been unwell since giving birth recently. He is somewhat taken aback by her assertiveness but appears to see the logic in John Proctor's argument that people are only confessing to witchcraft to avoid execution.
After Elizabeth is arrested at the end of Act Two, Hale tells John that he will testify for Elizabeth in court. He asks John to search his mind for the reason Elizabeth would be accused. Hale's instinct is to believe in Elizabeth's honesty and piousness, but as a Puritan minister, he must respect the proceedings of the theocratic court that will conduct the trials.