They're not against Charter Rights because section 1 sets out what is considered valid:
1. Canadian Charter of Rights and Freedoms guarantees the rights and freedoms set out in it subject only to such reasonable limits prescribed by law as can be demonstrably justified in a free and democratic society.
Protecting the public from a grave risk to their life and health in this case is demonstrably justified and therefore reasonable.
Canadian Rights are not nor have they ever been absolute rights. For that reason, the rules are not against the Charter at all. The correspond with the very first section.
I never said they were against the Charter, I said they were against our Charter rights. The opt-out clause isn't a "right" under the charter, its a loophole. As you say we have no guaranteed rights at all. Its the only way Trudeau Sr. could have made the provinces sign off on it. Quebec has gone around recently banning religious expression and free-speech/language rights for cultural reasons because it can. "Here's all your rights, but if your province wants to it can override every single one of them".
I'm not even saying the government curtailing these rights is the wrong thing to do, most of the time it has been the right move during COVID, but don't pretend that they haven't curtailed people's charter rights just because the charter contains an opt-out clause on every single right they wrote down.
"Demonstrably justified in a free and democratic society" is an extremely vague and subjective phrase, on purpose.