Indicate affirmatively that a credit card isn't an option for this payment, rather than opaquely allowing only bank payments
I'm fairly confident that the merchant has the ability to allow/disallow credit cards and that many merchants choose to avoid the extra fees associated with CCs. I'm sure you're passing any CC fees along to the merchant, and are pretty ambivalent about whether the merchant then chooses to allow CCs as a form of payment or not.
Only allowing bank payments is a reasonable decision for some merchants, but the invoice payment system should really indicate with certainty that a credit card isn't an option for those payments. Otherwise, users will spend time looking for the CC option, getting frustrated, and filling your ticket system with duplicate rants about accepting credit cards. The frustration will be directed at QuickBooks, rather than the actual decision maker (the merchant).
Just a thought...