Doesn't bother me at all.
What's wrong with having a provincial emblem on the helmets? If Sask or BC haven't done that, maybe the should consider it. So should the Ticats. As noted, the Calgary Flames do, so why shouldn't the Alouettes or any CFL team? Why is it more of a problem and less understandable if it's Montreal?
As far as the "nation" question is concerned, the Parliament of Canada passed a resolution a few years ago recognizing that Quebec is a nation within Canada. All parties voted for it. That is a recognized reality in this country.
Re the other issues mentioned, these are not relevant to football as a sport or as a business. Styling the provincial legislature as the National Assembly (Quebec), House of Assembly (Newfoundland & Labrador), Provincial Parliament (Ontario), or Legislative Assembly (all others) is a question of political protocol, not important to this discussion. Re. the size of the parade on June 24, so what? Toronto's biggest parades are Pride Week and Caribana. More Quebec flags than Canadian in Quebec?... yes, it's been that way for many years. Remember when Danny Williams took down the Cdn flag in NL during a dispute with Ottawa? Stop signs and parking tickets in French???.... yes, of course, people in Quebec speak French. Does Hamilton issue parking tickets in French, or in English only? Yikes!!
I think it's just fine that the Alouettes have the provincial emblem on their helmets. In fact I'm glad they do. I wish other teams would do it too. I propose the Ticats do the same. Let's put a trillium on them.