AFAIK the more higher performance beagleboards such as the X15 have native pci-e devices for sata, esata, ethernet etc.
I would suggest a more free device such as a BeagleBoard, the RPI foundation only likes open source when it is convenient with them (side question - how come so many laymen think it is an open source hardware?)
If you get a RPI for a long term project you're eventually going to run in to issues when support ends and the blobs no longer work with new distros/kernels.