I agree that replacements of note should be considered for Tony Awards. There are a lot of actors who would have walked away with one: Reba McIntire in ANNIE GET YOUR GUN, Dorothy Loudon in SWEENEY TODD, Bernadette Peters in A LITTLE NIGHT MUSIC. I'm sure many more worthy recipients could be mentioned.
But I doubt that in this case they would award a special Tony unless the producers hold undue sway over the nomination process (which seems doubtful given its poor showing last year).
I imagine they will give FUNNY GIRL a slot and allow Miss Michelle another chance of doing "Don't Rain on My Parade", which should sell more tickets than an honorary award.