How will you insure that a significant percentage of Tony voters return to see the replacement performance? What about other replacements that don't automatically have the cachet of JCM, who created the piece, directed and starred in the film, etc?
Back in the 1970s, Angela Lansbury took over for Constance Towers while Towers and Brynner were on vacation from THE KING AND I. For two weeks. Lansbury was brilliant, of course, but how many Tony voters could have seen her during her two-week run?
Just because replacements are sometimes sentimental favorites doesn't mean there's a fair way to administer a competitive category for them.
The special award to JCM is well deserved and an appropriate way to honor a very special "replacement" performance. IMO, obviously.