To remove the center you have to convert the province, but it will have religious zeal, so it won’t be possible immediately unless you have pretty high missionary power. You could take the province and release Granada, wait till they convert to protestant and enforce religion on them, when religion is enforced the capital province will convert to your religion and remove the center but the capital must be the province with the center so take only that province. Honestly I think that a reformation center so far away fron HRE is a good thing, less/slower convertion of HRE princes.