Analog off board connectivity
Seems like a sound approach to me as long as you are working with low voltages and sea-level/room-temp environment. You should make sure you understand the impedance of the SATA cable and that you are matching the impedance of the traces on your board and that you have a matched load. This is especially important if your signal includes high frequencies.

Also, you may want to make sure that nobody confuses your connector for a normal SATA connector, especially if there is potential to damage your system by doing so. I would consider adding some sort of additional keying, if possible, or at least add a warning label.