Is there a way to disable the ability to craft the Pocket Wormhole? If not, is that something that can be added as an option to the config?

Either use vanilla datapacks or something like CraftTweaker or KubeJS.

Could you add an option for keeping the Pocket Wormhole item but disabling the ability to teleport to waystones with it?

What would be the point of the item existing if it doesn't do anything?

In my case I would use it for the crafting the waystones themselves and only allow the player to travel using the waystones.

If you just want a blank item for crafting, you can make one with CraftTweaker or KubeJS.