Is there an X.509-based hierarchical bank registrar system for charge-origination signing certificates, for putting charges onto the card networks? Is there a DNS registry of merchant accounts for pre-checking charges before attempting them? Do banks underwrite other banks into existence by signing their certs?
In short, it's a different category of risk than the category that an individual business or even a business that is acting as a middleman for transactions takes on. And it's a different category precisely because most of the solutions aren't technical; they're legal, social, and financial. If a bank gets screwed it just gets screwed; even if the law intervenes to deal with transgression, money is often just gone as a result of such fraud. So they are comparatively more conservative in their decision-making.
This is probably what a business like OP's would need to do. When their customers are small, use a processor like Paypal or Stripe. But as customers get larger, OP should probably do what we did: partner with an ISO, who can get the customer their own merchant account. OP still does the processing for them, but the risk and finances run directly through the client, not OP. The ISO can also add in a margin on the transaction fees for OP if that's part of their business model.
Stripe makes this super easy, but it is a house of cards based on stories like this one. So I agree, you still need to get your own merchant account, and not rely on stripe as you get larger, but depending on your business model it might be taking more of your time generating due diligence documents than an acquisition.