Through The Crucible, how does Miller demonstrate how he feels about the witch hunter/trials of the 1950s?

I would add his adaptation of Ibsen's An Enemy of the Peopleas another, if lesser known, example of Miller's comments on the witch trials.  In Ibsen's play a doctor finds out that the health spas that are making his community "rich" are, in fact, poisonous are causing harm to the people who are coming there for help.  He thinks the community will welcome him as its savior; he is "shocked" when he is treated as a pariah, a threat to the well being of the general public.  They attempt to "reason" with him, cajole him, threaten him --- but he stands by his position, becoming, in his own words, "the strongest man in the town."

Miller is clearly standing by the position that the individual who stands by his values in the face of opposition, who cannot  be bullied by the powerful, is the only true individual.  Standing by your principles in the face of what he sees as the witchhunters at the Communist trials, is the only choice a real individual can make.