The current AF systems are going to perform more reliably than manual focus in most situations - especially those where you have limited time to get precise focus. The AF system of the D800/D800E is outstanding - but as mentioned it does show your misses. The D800 has more resolution than earlier cameras like the D700, and an improved AF system.
I'm not sure that Live View is practical for a typical portrait shoot - and I don't think it's needed. While the AF system used in Live View is slightly more accurate and .consistent than the phase detect AF used normally, the difference is small and much less of a factor than on earlier cameras. AF is one of the areas where new cameras have continued to progress.
The reason AF is dark in Live View is that your actual aperture setting is being used. Normally your lens is wide open for AF, so the viewfinder is bright. If you use the DOF preview button you see a dark view. You can open up the aperture for more light and then simply stop down as desired when focus is achieved.
I don't find the green AF light to be precise enough. It still relies on a number of variables. It's good - but not as good as Live View or even AF.
Finally, keep in mind the most accurate AF sensor is the center sensor. As you move out to the adjoining sensors and the edges, AF is less accurate and less reliable. Now they are still good - just not as good. If precise focus is required without fail, use the center sensor.