Creating, allowing and promoting Clickandbuy as a payment was a failure. Especially with the whole "no credit card option for you", it was clearly a lack of understanding/care of the player base. I'm sure there was some type of kickback involved.
Most likely, it was because SE had few options at the time, and was in danger of losing access to Credit Card payments entirely. Prior to the introduction of the system, FFXI had been hit by a massive wave of hacking and RMT-related credit card fraud, combined with chargebacks by unhappy players. Credit card companies will levy hefty fines against companies with excessive problems, or lock them out altogether.
If ClickandBuy is being discontinued, it is probably a sign that SE's reputation with CC processing companies has improved.