What really connects these two times is the idea of why people are being hunted. I would want my thesis to that idea. I would write something like this:
In both the Salem witch trials and the McCarthy Era, we see that unscrupulous people get ahead by using the fears of other people. These people, who are hungry for power of one sort or another, pick on some convenient scapegoats as a way of improving their own standing in the community.
This would tie how Abigail and Danforth, on the one hand, and Joe McCarthy on the other used the "witch hunts" to get more power and/or prestige for themselves.