I haven't read through all of the responses, so this may have already been addressed.
As a software engineer who works on a web application with a billing component to it, I feel I can shed some insight into this issue. The process for handling a credit card transaction is more complicated and involved than simply "paying the service fee" associated with running a charge against a card. There are verification and security issues to be addressed, in addition to having to support multiple different credit cards, currency exchange (particularly in international markets, as SE is), etc. this is why most companies do not perform the actual processing of a credit card directly but rather they rely on what are called a payment gateways--which more often than not tend to be financial institutions or companies with ties to a financial institutions.
Click and Buy, like PayPal have the financial infrastructure to process, charge, and credit various debit and credit cards. Click and Buy is an international organization supporting different currencies for payment and processing.
The odd thing that we see with SE and FFXIV is that they expose Click and Buy to the customer, something most companies don't do. Most companies interface with their payment processing partner and have a front-end that makes the process of paying for goods and services appear seamless and well integrated with the company offering said goods and services. For SE, this would have (should have?) been a web interface that integrated their payment services (e.g. Click and Buy) seamlessly so that the consumer (us) would never know what company was responsible for actually handling and processing all of the credit card transactions, unless we read the fine print.
Plain and simple SE isn't really doing anything different from a better majority of service and retail vendors out there, they just haven't obfuscated the process as much as others have.
Edit: I'm not going to get into the reputation of Click and Buy, others have already addressed that, I have my own opinions of SE's choice of payment gateway service, but that isn't relative to the part of the question you asked which was "why can't SE process the payments directly."


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