I too read the article, it points out some important signs of social dissatisfaction in Quebec, e.g. the permanent police strike, a general mistrust in institutions. This is not surprising given the massive corruption scandals over the last few years.

I find Potter's resignation very unfortunate for McGill: note he was not fired, he resigned from his position of director and is still a McGill professor. 

I am not worried about academic freedom . There is no way McGill could have fired him without a huge uproar. I'm guessing his colleagues at the Institute for the Study of Canada were so embarrassed by some of the far-reaching, one-sided statements in his article that they unanimously suggested he resign to save their credibility.

For example:
"Compared to the rest of the country, Quebec is an almost pathologically alienated and low-trust society, deficient in many of the most basic forms of social capital that other Canadians take for granted."