Want to whitelist commands? Take a look at
[CommandBlocks Extended +] Premium!
Person requesting this: http://www.spigotmc.org/threads/add-a-command-use-permission.50539
CommandBlocks Extended adds a permission node you can use in order to deny and allow players to use command blocks.
This is handy if you want to allow e.g. specific ranks (such as VIP) to be able to use command blocks, while disallowing normal users to use them. This also removes a security risk!
The permission node to use command blocks is "commandblocks.use".