Wojo was seen as the heir apparent, much like Mike Hopkins is the heir apparent at Syracuse. Wojo had been given the title of Associate Head Coach in 2008. He was next.
He could still be next, as you said... If he does well at Marquette he could certainly return in 3-4 years to take over Duke. But leaving leaves him open to the possibility of sucking, which would take him out of contention for a job that was more or less his to lose. That's why it's a surprising move.
Amaker is certainly an option now. Brey and Dawkins might be too old. But this move leaves the door open a bit for an outsider to get the job... a Shaka Smart or a Greg Marshall...
I just can't see Coach K doing this for too much longer, especially as his health deteriorates. I know he has said that he plans on coaching for at least another 5 years, but I just think his hand will be forced at some point. How many fainting spells can one man have?