It's rather more narrow than that. University professors were never muzzled, even if all of their research funding came via federal granting agencies.
The muzzling of scientists was limited to government scientists, i.e., those belonging to the federal civil service -- the ones whose jobs exist precisely for the purpose of giving advice to the government.
I'd say their jobs are giving advice to the public. Moreover the Harper party made it difficult for federal civil service scientists to communicate with journalists (aka the fourth estate of government) and the Greens, NDP, Liberals i.e. any other part of the government not in power. The Harper party overreach has no justification in a democratic society and you shouldn't be making excuses for them.
You seem to be getting government and parliament confused here.
Not even that. Canada currently has 338 MPs, 184 of whom are members of the Liberal Party; but only 31 of them -- the Prime Minister and 30 other Ministers -- are part of the government.
That is only the executive branch of the government.
That's sort of an odd way to frame it--it makes it sound like these people are only hired to interpret scientific literature for their superiors, or to conduct standard lab tests. On the contrary, many of these scientists conduct basic scientific research. There's no "advisory" value to that work--it is not intended for immediate policy decisions, but rather for the long-term advancement of scientific knowledge.
Basic scientific research is a collective effort, and the only possible outcome you could expect when preventing scientists from sharing their research with the greater scientific community is the prevention of scientific progress. Assuming rational actors, I cannot fathom another motive.
There was no such prevention.
Of course, there's plenty of time for Trudeau to get this wrong as well; he has his electoral blind spots as well.
The government is limited in its powers by Parliament and the judiciary -- the government cannot enact new laws or appropriate funds without Parliamentary approval -- but the government is nonetheless controlled by a small number of people.