Initially this story looked fairly simple: the Americans violating the sovereignty of an allied nation (Italy) to illegally kidnap and remove one of their enemies for torture in another country (Egypt). (So far, in these amazing times, the story sounds unsurprising).
It now appears that there's rather more to it than that. Despite the fact that he was involved with an Islamic Institute in Milan known as a centre of radicalism, he was in fact a CIA asset who had worked with Albanian intelligence. So it looks as if in fact he was the man who knew too much.
But further, it appears that there is a link between his abductors and the shadowy underground Italian neo-Fascist groups associated with the infamous P-2 masonic lodge and with the notorious "Gladio" group of agents provocateurs who were responsible for terrorist actions in Italy in the 1970s which were then blamed on the left.
Wayne Madsen speculates that the "too much" that he knew was related to current activities along the same lines: "Islamic terror networks" being run by the Americans for their own purposes. He also notes two parallels between events in the 1970s and recent events: the Bologna train bombing and the Madrid bombs, and the killing of Aldo Moro and the assassination of Rafik Hariri.
See also:
http://www.chicagotribune.com/news/nationworld/chi-050702milan,1,5108452.story
http://kurtnimmo.com/blog/?p=796
http://kurtnimmo.com/blog/?p=798
http://www.waynemadsenreport.com/diplomatic/foreign.htm
Local copy of Wayne Madsen's article.