I, too, am a little unsettled about the term "difference"; however, I think a minimal case could be made for differnces causing at least some of the trouble in Salem. A review of a few of the victims shows us evidence of that.
Giles Corey is different insomuch as he is both contentious and litigious. He's constantly taking his friends and neighbors to court, perhaps for perceived, or at least petty, wrongs. He's hard of hearing, so that may account for some of it; however, he's a bit curmudgeonly by nature, so it probably takes very little to provoke his ire.
Rebecca Nurse is different in that she truly is a godly woman--so much so that Reverend Hale, from another town, has heard of her good deeds and kindness. He even recognizes this godly character when he first sees her, noting 'you must be Rebecca Nurse.' What a high compliment, but what an anomaly she must have been in the town to deserve that kind of notice and attention.
John Proctor is different because he has the audacity to question godly authority. Rev. Parris is a mean-spirited, stingy man who cares more about money and things than the flock he is shepherding. Proctor recognizs this hypocrisy (perhaps because he's dealing with his own) and refuses to submit unquestioningly to this false authoirty figure.
Tituba is different for nearly every reason one can think of--ethnicity, color, class, religion...and the list goes on.
Others were poor or widowed or perhaps suffering from some mental distress which set them apart as outcasts. In any case, they were different.
I agree with the previous post because of the use of the term in question. I think an argument could be made that "sameness" is the cause of all conflict in the play. Abigail's desire to want to be the same as the other women who were happily married with husbands like Elizabeth causes her to covet John. At the same time, the accusations made about Tituba were deliberately targeted at her because she was different from all others. In fact, the entire premise of accusing others of being "witches" is an accusation that is rooted in the idea that everyone possessed a horrific fear of that which is different. Sameness is what is preached. It is not as if people were told that differences in worship is a morally acceptable outcome. The leaders in Salem banked heavily on the fact that the pursuit of only one moral end, one that did not include differences in perception or spiritual worship, would galvanize people to be afraid of witches and place all of their trust in the leadership. The very fact that individuals like Corey and Proctor are killed is because of the desire for sameness, that they did not capitulate like so many others. Difference is actually morphed into the desire for sameness.
"Difference" is a pretty vague assertion to start with, as it can mean so many possible things. A difference in ages between John Proctor and Abigail Williams? A difference in status between the townspeople and the Court? Between Mary Warren and John Proctor? So in these ways, sure, difference can be the root of all conflict in the story, but I don't think that's saying very much.
I tend to agree more with the statement you follow your question with about the various emotions at play in 1692 Salem, with fear being the primary one, followed by jealously, lust, superstitions, etc., as the real causes of the conflict we see in Arthur Miller's play.
While there are some other possible references to "difference", such as Putnam's land disputes with Giles Corey and John Proctor, or the arguments between the townspeople, even the differences between peoples and classes in the testimony at court, I simply don't think it's a very specific or accurate way to characterize The Crucible.