It can be amended of course, but you mentioned bending the laws to accomodate religion. I'm just setting that part straight. The laws (in Canada) aren't bent to allow for religious freedom, they guarantee it.
It's worth considering the material conditions upon which the Charter was created. Religion was prevalent and religious people wanted to be free from being persecuted for their religion. Today irreligious people in Canada are about a third. If we amended the Charter to curb public religious display, it would go against the majority of Canadians. That's undemocratic, and unrepresentative of the reality of the country. If some gov did that, it would likely experience severe backlash and the changes would be reversed to more closely match the material conditions.
I'm also an anti-theist and would love religion to disappear, but I think that cannot occur through repression via law or other means. Rather people of religious cultures have to go through the material evolution secular societies have. The Eastern bloc did a lot of work to repress religion without addressing the material conditions giving its rise. Now irreligious people are still a minority in those countries.