I did a study of storage solutions for a rugged system a few years while ago, and indeed one of the reasons why we chose the S-Tec compact flash card was the much easier to implement PATA interface.
There seems to be a sata host core (
http://www.altera.com/products/ip/iup/additional_functions_iup/m-intelliprop-sata-host.html) available, apparently you'll either need a FPGA with integrated transceivers, or use an external serdes. I'm sure that if you contact IntelliProp they can give you more information about what is supported.
I'm also rather sceptical about the SATA connector under strong vibrations, it looks rather fragile. There could be a rugged version now, but there wasn't at the time I did the research.