Just finished watching the episode.
The Doctor was deactivated when he asked why there were two Keses, but Kes, Tuvok and the Captain entered into a secret conspiracy to save the future and save B'Elanna (Tuvok had a vision of her death). Kes was mostly asleep as gammy Kes dragged her to the shuttle bay, but she would have had full access to what happened after the fact.
The corpse was not disintergrated, but if it wasn't given to the Doctor, what happened to it?
Having her first strike (both times) during Tuvok's birthday makes me wonder if Gammy Kes saw that as the last straw for some crazy reason?