I have the premium version from here.
The issue persists in the 1.6.5+fix version as well, but the option is there when i use a save from a year ago.
I just checked the code for the three premium version on the website and none is censured — the only way the Punish option could disappear is if a certain variable is turned on, and that variable is only turned on in the Patreon version. Are you sure you're not playing on a save created on a Patreon version? I can't really think of anything else that would explain it.