I don't have any problem with using the 100mm USM macro in autofocus. I find that it is really fast and suitable 95% of the time. The other 5% of the time I use the manual focus override, and since I never shoot with focus on the shutter, it's always there for me if I need it. I also sometimes move the focus point off center to match the eye in whatever composition I have framed.
AND, I also often focus to a pre-set distance and move in and out until the eye of my subject is in focus (or, slightly in front of the eye if the subject has a long nose). With the 180mm, manual focus and moving back and forth is the only way to do it. 
On this last trip to the Solomons, I spent 45 minutes watching two pygmy seahorses on a gorgonian. I had the 180mm and was able to stay far enough away from them so that they went about their business without being threatened by me, but I had to sit there rocking back and forth in minute motions to keep the eye sharp while waiting for them to do something (like move. ). In 45 minutes, one of the jumped to another branch four times, and I managed to shoot three of the incidents, moving backward a bit to anticipate the movement of the pygmy toward me before shooting. There is no way I could have used autofocus at the time to get these shots; moving back and forth and using manual focus was the only way!
Neither the 50mm Sigma nor Canon macro lenses have FTMF, unfortunately, but I haven't needed manual focus with the 50 yet. BTw, I use the Sigma because it focuses 2x closer than the Canon.
