Doogie,
It has been several years since we stayed at Hotel Sonya on our "Rick Steves Heart of Italy Tour," and perhaps someone who has stayed there more recently can provide more updated info.
My recollection is that it was a very, very clean hotel, and I do not recall a "doggie smell." But, that said, it is also my recollection that there were both hotel rooms and privately-owned condos in the building (at that time). So, if that is still the case, there might be the chance your wife could wind up in the elevator with a condo owner who has a dog (or if the hotel allows dogs, then another guest with a dog in the elevator or stairs).
Some hotels seem to allow dogs in just certain rooms or certain parts of their hotel; and if that is the case with these hotels (I have not idea), then maybe you could request a pet-free room.