So that would mean then that the provincial governments don't have the authority to quarantine healthy people either then?

Nope. Provinces and feds have different kinds of authority. The feds can only quarantine people which come into Canada, but they can't restrict travel within a province or between provinces. But provinces have through Section 1 of the Charter a way to restrict travel within their borders and thus override Section 6 of the Charter.

https://www.cbc.ca/news/canada/newfoundland-labrador/nl-travel-ban-supreme-court-decision-1.5727549