It is not so much to stop those that want to purposely cause harm to the server, that is near impossible to stop. It is to prevent those who do not know better from logging on with a mod on their client that many cause lag to the server.
On the FTB server that I admin on when I logged on with Treecapitator it caused the server TPS to drop from 20-12. If it was someone else who had the mod on their client i would never know and the server would just be laggy, If there was a tool to allow only certain mods then that could easily be prevented.