Back to the original question...
I just got back from a research trip on which I had several chances to use my new Canon 100mm USM lens. It's an amazing lens.
Before the trip I'd posted a similar question about zoom macro in general: do you prefer AF or MF? I got a few answers with varied opinions. Now I suspect the opinions varied because the folks responded were shooting very different sorts of subjects.
Here's what I think now having taken a few hundred shots with this lens:
MF is close to useless if you want to shoot things that are very active, like small damselfish. With the incredibly shallow depth of field inherent to zoom macro, you just can't turn the focus knob fast enough to keep up with the subject. AF does an excellent job for this unless you're shooting something with low contrast (e.g., an all black fish) and here it fails miserably. Consequently, it's helpful to have the ability to switch to MF when necessary (but if your subject is small, black, and moving fast, you might as well just give up and find something else to shoot). Provided you're shooting well lit subject with good contrast, I can't imagine why you'd want to use MF.
The humble opinion of someone who's only owned an SLR of any type for 4 months.
Mark