it's fine to say that kes wasn't popular... but who was?
Seven wasn't a break out character, she made out there, or broken, I'm not sure which, it was cheating either way.
So if Kes stayed, would Tom have wound up with Kes or B'Elanna?
Because before and After had some mighty strong opinions about Year of Hell.
Kes jumping queue to mount Tom changes future history and saves B'Elanna from being killed during first contact with the Kremin. It was completely selfless of her to disrespect B'Elanna's heart to save her life.