$> sudo libinput-list-devices
...
Device:           TPPS/2 IBM TrackPoint
Kernel:           /dev/input/event8
Group:            9
Seat:             seat0, default
Capabilities:     pointer 
Tap-to-click:     n/a
Tap drag lock:    n/a
Left-handed:      disabled
Nat.scrolling:    disabled
...

The last line shows that it's available but disabled. Quick git log shows we've had natural scrolling for all pointer devices since 0.7, so you just need to figure out how to enable it in your configuration :)

xorg.conf snippet for X, under a wayland compositor you need the compositor to support that option.