It's not something I remember encountering in the one time (so far) that I built this on Apple. When I Google your error, it suggests that disabling SSE would probably remove the Intel-specific flag. The niftyreg functionality mri_reface is using doesn't require any of the optional features, so for any niftyreg build problems I would disable whatever you can via cmake (here, SSE, but if errors with libjpeg, disable jpeg, etc.) and try again. The "ccmake" GUI interface to cmake would help you see what options are available. 

Chris