We have QB and Evalon. Elavon has much better rates but QB's can do ACH pulls. We typically turn ACH on first and if the customer requests a CC payment option, then we will enable credit card payment within the invoice. Way more convenient than a typical processing company.
It does suck with a customer wants to pay a $30k invoice via CC but that's the cost of business. As others have mentioned, add 2.5% to all estimates and offer a 2.5% discount if paid via check. It's just more back-end work to handle this philosophy.
"Just when I thought you couldn't possibly be any dumber, you go and do something like this... and totally redeem yourself!"