Title.

If you don't want an item to be craftable, have some kind of toggle that sets the UI to remove mode.

In the UI, you can either put the item directly into the output slot and hit Remove, which will remove ALL recipes that output said item, or (if multiple mods add recipes for an item that you're removing) input a recipe and the output item and hit Remove, which will prevent that recipe from making the item.

Unfortunately, neither of these approaches are feasible. I can however look into adding an option to generate a recipe file that overrides an existing recipe such that is effectively removed by having you give the tool the original recipe's name. If I recall correctly, JEI shows you the name of the recipe you are looking at somewhere, so you have options to find that out.

This should depend on either CraftTweaker or KubeJS then as they're far more powerful, Vanilla's recipe system is very limited.

Both mods also have addons for other mods.

The whole point of this mod is to generate datapacks and not scripts that hack the datapack system (completely ignoring the fact that it's significantly easier to programatically generate JSON files than JavaScript or ZenScript code).
Apart from that, Vanilla's recipe system is powerful enough.