Ted here from Shopify, thanks for reaching out to us!
This is a great question! You should be able to deactivate the gateway by selecting Settings > Payment Providers > Shopify Payments > Manage as shown here in your admin. From there, you will then need to scroll to the end of the page and select the Deactivate Shopify Payments button as shown here.
Shopify Payments applies a lower credit card fee when it's used in comparison to third party gateways such as Paypal. More info can be found here but I'm happy to offer an example of this if you would like? If there's any feedback as to why Shopify Payments does not suit your needs, I'd be happy to forward this information to the team for future reference. Any extra info is welcome!
If there is anything else I can help you with, please let me know, I'm happy to help!
Thanks a mill,