With respect to individuals, she could make a decision, and as long as it didn't result in sending someone back to torture it wouldn't be inconsistent with the charter, but it would allow her to make a decision with respect to an individual applicant.
With respect to classes or categories of applicant, it's interesting that you invoke the charter, because a lot of these applicants are outside of Canada. Indeed, the Federal Court has said that with respect to immigration matters, the charter doesn't apply to applicants outside of Canada. So the charter wouldn't necessarily be a remedy for someone if the minister issued an instruction outside of Canada.