Via the Yale Alumni Magazine :
If you were especially observant during your years on campus, you may have noticed a stone carving by the York Street entrance to Sterling Memorial Library that depict a hostile encounter: a Puritan pointing a musket at a Native American (top). When the library decided to reopen the long-disused entrance as the front door of the new Center for Teaching and Learning, says head librarian Susan Gibbons, she and the university’s Committee on Art in Public Spaces decided the carving’s “presence at a major entrance to Sterling was not appropriate.” The Puritan’s musket was covered over with a layer of stone (bottom) that Gibbons says can be removed in the future without damaging the original carving.
The obvious point seems to be that "Puritan pointing a musket at a Native American" seems inaccurate. They are both looking in the same direction and one would expect the puritan to be looking towards the indian if the intent was to aim at the indian.
They do get one point of credit for making the censorship of the past both largely unobtrusive and reversible.
The only quote of the head librarian Susan Gibbons is "presence at a major entrance to Sterling was not appropriate" Unfortunately there isn't any explanation of why it is inappropriate although one might assume that the "Puritan pointing a musket at a Native American" canard might be why.
I'll note that the Committee on Art in Public Spaces self description is "The committee will hear from members of the community about art and other symbolic representations related to diversity and consider ways Yale might better reflect our campus and our history."