We have found a few work arounds that have helped us ensure we aren't inadvertently charging customers credit cards when receiving payment due to the default enabling of payment by credit card. 

Update Payment Methods - this step allows you to adjust your payment methods to ensure only credit cards prompt for automatic payments. 
1) Search "payment method list" - this gives you a report with all the payment methods available in your organization (but no option to delete or make them inactive unfortunately).

2) Edit each payment method to ensure the "This is a credit card" box is only enabled for credit cards. (For some reason nearly all our payment methods had this enabled, I'm not sure why, but it was before my time at this organization).

Update Customer default payment methods - this step allows you to adjust the default payment method to act as a double check before charging a credit card on file.

1) Navigate to the customer

2) Select Edit and scroll to the payment methods

3) Even if their default payment method is a credit card, change it to a method that is NOT a credit card. 

This ensure that if we want to process a credit card payment for the customer, we manually have to select credit card when receiving payment. We prefer the extra step to ensure we are processing the payment correctly. This is also a safe guard for customers who do have a credit card on file, but don't necessarily use it as their default payment for all invoices.

It's not perfect, but it's working for us.