Haven't they heard of Stripe? It's really easy to use Stripe. They should just use that. I'm not sure they looked at all the available solutions out there for processing payments.
If they have high dollar value deals that are just as easily paid via low-cost bank debit, Stripe's 2.9% can be expensive. A $5,000 invoice paid through Stripe (at default rates) is $145.30. If you are billing a recurring $50/mo for a service, the fee makes sense. But one-time PO payments may not over a certain $$ figure.
Nope. You just save a token for that transaction, and tell your processor you'd like to refund that transaction. They have the associated card on file, not you.