I've played the original Crusader since back in the day and enjoy its balanced gameplay. Extreme however is a bit too beyond my skill level, and the balance feels somewhat broken. I've tried uninstalling Extreme, but that removes Crusader as well. What are my options?

Hopefully GOG can address this in an installer patch. :/

Why is uninstalling it so important? Just delete the shortcut off your desktop if you don't care for it.

If it absolutely must be removed for some reason, you could manually delete the "Stronghold_Crusader_Extreme.exe" file and the "maps extreme" folder from the installation directory.