So you are suggesting that there is in fact only one way to amend the succession and that is to amend the constitution under Section 41. Yet if you read this G&M article:
http://www.theglobeandmail.com/news/politics/ottawa-notebook/harper-backs-british-pms-plan-to-modernize-royal-succession/article2199964/
OF COURSE an amendment under Section 41 would not be subject to Charter scrutiny (I never suggested otherwise), BUT - it seems pretty clear the PMO does NOT favour a constitutional amendment. And for good reason - the odds that all ten provinces will ratify an amendment that elimiantes the sexism and allows heirs to marry Catholics yet still blatantly discriminates against future Catholics acceeding to the throne are less than zero. In any event, it seems quite clear Harper is not willing to reopen the Constitution over this.
The PMO view appears to be that if Parliament can pass a law that amends the succession to the Crown, that in itself does not alter the rights and perogatives of the Soverign, it simply alters who the future Sovereign might be. And that, in the apparent view of the PMO, does not require a constitutional amendment.
But any new Act of Succession that does not amend the Constitution is, in fact, ordinary legislation that is bound by the Constitution, including the Charter.
Of course, a succession amendment enacted by ordinary Parliamentary legislation that both eliminated gender preferences AND permitted heirs to accede to the Canadian throne regardless of their religious affiliation, including Catholic heirs, would have no trouble with the Charter. Whether it would withstand a challenge under Section 41 of the Constitution - the PMO seems to think it would - personally I do not know.