I added this to an existing game where military science was already researched--and the toggle for whether you can craft it doesn't do anything, the only way to get it is to kill biters.

Hello, sorry for late response ( In past months I visit mod portal on ~monthly basis )

As I tested it similar, but opposite bug happened to me - no matter what was set in settings - recipe kept being available.

I think I misunderstood how technologies work... So I changed way in which mod works. Now enabling option "disable crafting" no longer modifies technology so it doesn't unlock recipe. Instead enabling this option causes recipe to take 0 ingredients, produce 0 mil science packs and to be hidden. Mod no longer touches technology itself... Which might break some compatibilities and/or enable other compatibilities... For better or worse.

After testing it by starting sandbox game without mods, then researching all technologies and only then installing mod - it worked as expected (switching this option switched availability of recipe).

I hope this will help you (even though you had a bit opposite issue)