As the title suggests, it would be very nice to be able to disable the indestructible enchantment completely in the config for balance reasons.

Yes, please add this config option!

Totally, agree. Been looking for a way around this, but only way i can find is just making the recipe harder, which would then negate the repair function of item

If you don't want the indestructible enchantment you could simply remove the recipe that applies the enchantment (apply_indestructible_enchantment.json).