I'm not too sure that those are the only choices. I guess that's why I'm struggling with your question.
I would think that if there were an issue that the Canadian Human Rights Act in its entirety is somehow problematic for whatever reasons from a first nations community viewpoint, then rather than piecemeal picking of an act that they didn't draft in the first place, a more sensible resolution might be recognizing their jurisdiction to enact something that works that is also consistent with international human rights law.
You do see references to international human rights law in self-government agreements. For example, if a first nation government enacts a law that creates an issue internationally in terms of compliance with international human rights law, the more recent self-government agreements provide for processes for Canada to discuss that with the first nation or aboriginal community concerned to resolve it, so that Canada collectively is in compliance with international human rights norms.