Sadly, it's a complicated mess especially when regulations are factored in.
For one, it might be helpful if you forget about swiping cards (i.e.,
manually enter information... perhaps on a computer running Trisquel.) There
is a list of payment processors on
https://snowdrift.coop/p/snowdrift/w/en/payment-services with some notes and
information.
Patrick McDermott, aka pehjota on IRC, has developed a free replacement for
the proprietary JavaScript needed by Stripe:
http://www.pehjota.net/projects/epirts.js/
But this is only for the payment side. It does nothing for the proprietary
software that YOU as the owner would need to run when logging into the site
for reporting, etc.
Plus, issues of PCI DSS compliance come up. You should REALLY be talking to
pehjota about this subject. He has done much research in the area of credit
card processing in the free world.
