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Since BETA 3.2 Perks can be locked. You can find a boolean statement named ALLOW_LOCKED_PERKS in InternalSettings which states if perks can be locked or not.
To lock a perk go to perks_init and add the following line (change the name ofcourse), this will lock the perk for all storylines:
ChrPerksList.list.PERKNAME.locked = true;
Gain a gouvernors trust to enable this Perk. (The crop yield is 50% higher on the character's estates)
If you want to know if a perk is locked or not you can use the following command:
When you want to unlock the perk use the command: