No, that's not the case, because it's important to clearly distinguish between the language of work at universities and people's native languages. Some people can work in their discipline in English or French. However, people in most disciplines work in English, particularly in the natural sciences and physics. It doesn't matter whether people are francophone, Portuguese or Hispanic. The language of work is English.
Analyzing the SSHRC data reveals that francophone universities, in the institutional sense, aren't at a disadvantage compared with anglophone universities. In fact, the U15 association isn't necessarily the most relevant group when it comes to addressing this issue. For example, the Université du Québec à Montréal is in a good position at SSHRC because it has a great tradition in the humanities and social sciences, even though it's a public francophone university that could be considered a far cry from a university like McGill.
While the most prestigious universities are definitely anglophone, that doesn't mean that the dichotomy between francophone and anglophone universities makes it possible to understand the disparities that occur or that reoccur.