How to efficiently separate bad from good pomegranate arils?
I always cut the skin along the ridges as described in this answer to your referenced question. This has the advantage of breaking the individual segments out of the fruit mostly undamaged (with all arils still in place). 

Once you've broken loose a segment, it's easy to seperate the arils from the white flesh by gently brushing your fingers over them. If there are any bad arils around, you can either leave them in the segment by not brushing them loose or you can dispose them into a seperate container.