Is there a flag to tell Embree to only return hit intersections for "one sided" triangles
I.E. If the triangle's normal was pointing away from the casting ray, opposed to if they were in opposite directions.
I don't believe so. You need to use the filter function and test which side of the triangle was hit and discard those hitting the wrong side.
Compile Embree with the RTCORE_BACKFACE_CULLING cmake option enabled, and all back-facing triangle will be ignored.