Was the death count ultimately negative? Let's think... oh, spoilers ahead.
By stomping on Quan Chi's nuts, Scorpion, Sub Zero, and Jax were resurrected. Scorpion deserves special mention since in basically every single game up until this point he was ALWAYS undead, the Ninja Specter. Now he's alive? Made peace with Sub-Zero? Resurrected the Shirai-Ryu with Kenshi's help? So we have four points off the death count.
But people who were killed on screen? You've got Mileena, Quan Chi, and Quan Chi's nuts which were sacrificed so that others may live. Shinnok was still alive at the end despite being significantly shorter, but otherwise? Only two named characters die on-sceen, and useless mooks who die in droves don't count.
You're right.
Mortal Kombat X's FATALITY Count In-Story: -2. It only evens out to 0 if you count Quan Chi's balls.