I tried it on my friends ipad (dont have one of my own) and it works when launched from the homescreen. Clicking the download link opens a new safari window with the filename and an "Open in iBooks" link. Clicking the link opens it in ibooks.
The only thing I can think of is if you have authentication turned on. That might make a difference, because safari wont know the username/passwor, although it should still just prompt for them.
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