Saving this here so it’s less trouble to find in the future. Ten years later and there’s still no generic means to accomplish this most simple of tasks without device specific junkware except via registry hackery.

Get-ItemProperty HKLM:\SYSTEM\CurrentControlSet\Enum\HID\*\*\Device` Parameters FlipFlopWheel -EA 0 | ForEach-Object { Set-ItemProperty $_.PSPath FlipFlopWheel 1 }

From superuser.