I agree with you, the polygraph is a interrogation tool, not a "lie-detector", hence why the GBI does not want it videotaped. On the best of days, those things are only 50/50 and very subjective. Nonetheless this whole case does have a Scott Peterson ring to it.
This one is easy. Get three GA Tech linebackers and let them spend a few minutes with the boyfriend discussing her whereabouts. Besides a shattered spleen and 14 broken ribs, I predict a quick full confession.