There is an option for one-time use credit cards when creating transactions and for customer portal users to use when paying an invoice.
You can see this on the New Payment page (Accounts Receivable > Invoices > Pay Invoice button in the grid). This is the Save Payment Details switch:
By default, this is set to YES, which means that credit card details will be saved as usual. Setting this to NO will prevent the existing credit card/eCheck information from being selected by disabling the Credit Card field. When clicking the Submit Payment button, a new window opens and the entered credit card information will be submitted without saving it for the selected invoice amount.