SE most likely have to pay fees to click n buy for using their product, so the visa fee has nothing to do with it, just like how they have to pay paypal as well.

SE did handle CC info, in XI, but it wasnt a very good system, its much easier to outsource to a company that is dedicated to just CC info.

Also the PSN incident has not much to do with it, the people who obtained the personal info did it to prove Sony suck, and they wont do anything with the information, they're on the side of the customer since Sony has no customer relationship. Also the CC was encrypted.

You can already use prepaid cards through paypal, so I dont know why you are suggesting a feature that already exists.