Switching "TrackpadMomentumScroll" on and of using a script
Oh, found it. You'll have to reload the appropriate kernel extension like this:

defaults write com.apple.driver.AppleBluetoothMultitouch.trackpad TrackpadMomentumScroll -bool false

sudo bash -c "kextunload /System/Library/Extensions/AppleBluetoothMultitouch.kext; kextload /System/Library/Extensions/AppleBluetoothMultitouch.kext"


After that your trackpad will shortly become unavailable, but will be reconnected and have the MomentumScroll setting.

This still isn't, what the System Settings-App does, because you'll have to enter your password for sudo (and be an administrator), but still it works.