As of release version 0.13.2, negative scrolling multipliers in kitty.conf aren't applied properly in vim. I have narrowed the problem down locally to this merge.
For reference I am using a touchpad on a Dell XPS 9730 on Arch Linux. The reverse multiplier seems to be applied fine in other applications such as less. I also have both wheel_scroll_multiplier and touch_scroll_multiplier in my config both set to a negative value (-3).