People don't call people "Ms." anymore, and certainly not informally. It's a very formal aloof title, not suitable for coworkers or friends. And putting it with a codename is even more odd, like calling Cap "Mr. America" in order to clear up confusion. The only way 'Ms. Marvel' sounds natural is as a jibe coming most likely from Tony... and having that stick would be a bit of an injustice, I think.
One way to follow up the Tony Stark eye roll and put the issue to bed:
STEVE ROGERS: We always had multiple Captains in our division, and no one ever got confused... how about you, Major, did you ever get confused with multiple Captains?
CAROL DANVERS: No, Captain, I did not.
STEVE ROGERS: Me neither.