Yes, I not only read your post, I read the decision of the Supreme Court in R. v. N.S.

In it, the  Charter right to a fair trial prevailed over ("bowed to" in your words) the Charter right to freedom of religion.

Absent that conflict, her Charter right to freedom of religion allowed her to give evidence - in a public court - wearing it.

It's hardly "end of story" - a court would ask what other Charter right prevails in each instance of giving or receiving a public service.  For instance:

What Charter right prevails over a niqab-wearing woman getting a library book?

I'm betting you can't come up with one.