Simply, the Charter treats the individual, and not a group, as the basic legal unit of society, so a group cannot have rights distinct from those of the individuals it comprises without compromising the principle of equality before the law. We have tons of exceptions already (children, women, peace officers, protected classes, lawyers, refugees, etc.), but these bend and decorate that principle and are inconsistent with it in places, but we muddle though.

There are no short answers, but since you've asked - Essentially, the rule of law has no business in the lives of a "community," and while the freedoms of speech, movement, and association allow a community to pursue their collective interests, those interests and rights are limited by the equality of the individuals that make up the whole society. It's an imperfect dynamic, but the alternatives are 20th century history.

Remember that freedom is different from a right, in that a freedom represents the limit on an external human/state power, where a right is something given and enforced by one. A right is just permission, which reinforces the power of the grantor. You don't have rights to freedoms, you have freedoms that the rights of others balance. (to say you can be free from hunger or forces of nature, is essentially a misuse of the term because there is no other person involved) In this taxonomy, taking liberty is the act of exercising both rights and freedom.

In this sense, communities are not, and cannot be free because they are not individuals, and to limit the power of a nation state to impose rules on a community (to free a communuty), creates a an unequal class just as privileged as one given special rights. A community can be granted rights, but very sparingly, because every single one has to be weighed against the necessary compromise it creates against the principle of legal equality. (The notion of "human rights," is its own issue because it implies a universal earthly grantor and enforcer, which you can appreciate the complexity of. Originally they were called "human dignity," which was more practical, but again, different can of worms.)

If the communities I live around want to collude to restrict my nationally guaranteed Charter rights of movement, association, and making a living using an internal compliance passport, it's illegal, but there is still a legal mechanism if they want to push it, and it requires passing legislation with specific prescribed legal tests, which this govt has not done. Instead, this govt (federally, and provincially) has abused "temporary" emergency powers to normalize abhorrent 20th century internal passport systems that violate Charter rights, and stepped out of their mandates into attacking freedom - which means overstepping its authority and voiding the entire social contract.

This idea that science (and not, say, math) overrides our Charter, legal system and social contract is necessarily absurd because science is how we discover and organize knowledge (or lately, produce narratives), and at it's base level, law is how we agree not to hunt each other for sport. They can enlighten each other, but they can have no power over each other that reconciles to truth.

Using this medical emergency to contrive exception after exception to unmoor our society from these limits on state power so as to be able to privilege the "communities" that prop it up at the expense of the rights and freedoms of all individuals has been a clever application of a specific theory, but they've broken the rules.

Hence, I'd say the question of balancing freedoms of individuals against those of communities while preserving the integrity of the principle of equality is a false dichotomy, and is a begged question for the legal legitimacy of a community as a thing at all. So, get shots, wear masks, stay home if you want to, don't invite wrongists to your house, but otherwise, we're equals, so farewell and good luck!