In this hypothetical situation you've set up in which Visa somehow knows that one of their billion+ payments is for the contract killing of another human, then no, it's probably better to not let the payment go through.

However I find the argument you're posing apparently in favor of allowing a business like Visa to decline transactions on ethical grounds to be missing some important rigor. It's honestly kind of boring to argue about very clear-cut and extreme example like a credit card payment that is clearly for a contract killing. That's not where the meat of the issue lies.

If you'd like to make the argument that a business like Visa should decline transactions based on the ethics (as opposed to legal & financial risk, which appears to be how they do it now) of that transaction, then I think you need to come out of the gate with a bit more rigor. Here are the questions that immediately come to mind for me:

1. Can we agree that the rules applied to a multinational corporation with billions in income utilized by hundreds of millions of people on a daily basis to exchange legal currency for goods and services should be different than the rules governing the bakery down the street?

2. If yes, then within the context of multinational financial corporations, what is "ethical"?

3. Who decides what that definition is for a multinational financial corporation?

4. Is that definition industry-wide or specific to a corporation?

5. Is a corporation expected to hold to a consistent definition of "ethical"? If they are, how is that enforced?

6. If a corporation is not required to hold to a consistent definition of "ethical", how is this different from "for any reason or no reason at all"?

7. If an individual's small business is deemed "unethical" by a monopoly or near-monopoly, such that it is impossible _in practical terms_ for the business to exist based on an extralegal decision by a multinational financial institution, should there be any recourse for that individual? What would that be? Over what timeline could it be reasonably accomplished?

8. Remaining firmly in the context of applying your above answers to multinational financial corporations: how do your answers create a net boon for society? Who is likely to benefit from your policies? Is there any apparent harm from your policies? Is that harm a net boon for society? How and why?

Without some thought put towards these questions, or ones like them, your (apparent, there's not a lot to go on here) proposal of universal ethical freedom for all businesses looks a lot like "unlimited freedom without regard for how that unlimited freedom affects others." Which, if you are seriously putting that argument forward, I'd like to circle back to contract killing and ask what damn right does Visa have to limit one's freedom to run a contract killing business?