Am I the only one who remembers the Alternate Universe Ms. Marvel/Warbird from MS. MARVEL #9 and #10? That Carol was defeated and taken into SHIELD custody. And it stands to reason that SHIELD wouldn't just keep a perfectly good (if slightly homicidal) Ms. Marvel on ice. Maybe they hypnotized her as a sleeper agent to be activated if needed, and that little tidbit was carefully hidden from Norman during the HAMMER turnover.