All the recipes made in the crusher are still being registered and shown in JEI after I disabled the crusher in the configs.

Can it be made to not register the disabled blocks and it's recipes or at least not be shown in JEI?

Thanks

No, sorry. The config only disables the crafting recipe, not the feature.
Disabling features is not something that I want.
You can use JEI's hide mode to hide the Crusher though.

By the way, you can use ModTweaker if you're in 1.10 to disable Crusher Recipes.