You don't have a lot to choose at the intersection of open source and PCI compliant eCommerce platform. One option that I know is Zen Cart. The out of the box front end and back end might not be intuitive (read ugly), but the platform is highly customizable. So your dev team would have to put in some effort here. Do note that you'll get hundreds of free plugins and support from the forum (also there is a wiki).
For PCI compliance, you would have to take care of the the hosting environment (stuffs like deactivated weak cipher and updated OpenSSL), payment provider apart from the platform itself.
Good luck!