First of all, Peters' Tony nod for Sunday was around five years before ITW. In between the two, she actually won the Tony for SONG & DANCE.
I believe Peters was only in the show a relatively brief period of time (can someone confirm), having agreed to do the role to get Sondheim and Lapine out of the jam of losing their original choice for the Witch (Betty Buckley...again, can anyone confirm). There was also a feeling that the Witch was more of a supporting role (as Frank Rich put it, 'a small but beloved turn' in reference to Peters' performance).
I do not believe having her present the Tony for Best Actress in a Musical that year was a slap in the face. It allowed her to joyously present the award to her esteemed co-star. Peters, always the very definition of grace and class, I'm sure was truly delighted for Ms. Gleason's much deserved win.
"I'm so looking forward to a time when all the Reagan Democrats are dead."