I've disabled alost all payment modules when in store pickup i set as shippemnt. I'm using for this plugin for Magento\Payment\Model\Method\AbstractMethod and is working fine.
Only one module payu/magento2-payment-gateway that i cannot disable. it is not using Magento\Payment\Model\Method\AbstractMethod
Maybe someone can show how to disable it in js? I've tried to hide it when some one chose shipping method, but payments options do not exist yet.