Is it possible to run Google NaCl outside of the browser as a process sandbox?
The Native Client documentation is probably a good starting point for trying to figure out how everything works.
As Mark Seaborn and Bennet Yee indicate, you are probably best off looking into using sel_ldr. More details about how sel_ldr is included in "The life of sel_ldr".
I haven't personally implemented anything that uses NaCl outside of a browser, so I can't unfortunately comment on the ease of doing so.