After reading the National Memo article it doesn’t seem like the 54th Monument was desecrated by the CS flag, but rather enhanced:
The battle flag was found Sunday night attached to the memorial for Colonel Robert Gould Shaw and the Massachusetts 54th Regiment — the first black troops organized in the North during the Civil War — with the flag having been placed over the sword on the figure of the white commanding officer Shaw.
The point of a Yankee sword just seems like an appropriate place for that flag.