I experimented with a gateway system from Wells Fargo some yeas back, but it was more trouble than it was worth for my small operation. Today, I just use PayPal -- there are overhead costs, but there always are, and people are familiar with it. If I started actually selling something, I would go with one of the packaged "store front" options (I know of Yahoo and Amazon. I'm sure there are others).
Kickstarter can also be viewed as an e-commerce system when it is used for "pre-sale" campaigns in which the "rewards" are basically just copies of the product to be produced. They actually get their money through an Amazon system.
Not sure about the "social consciousness" of these choices. The way I see it, though, is that if you're taking money online, you're dealing with bankers, and that's unavoidable.
Am interested in hearing about better options if they exist, though.