Yes, Peter did manage to keep his name out of all the scandals his entire career, and that 1996 Tour was by far his best ride. But in those times, I would have a hard time believing anyone even finished that Tour clean. Still, he should at least somewhat be commended. By a similar token, Charley Mottet morally won the 1991 Tour, and Giles Delion won the 1992 version, as it's pretty well assumed those were possibly the only two clean riders during that era.
I actually started looking at top 10 finishes in recent GTs and came across some more names that haven't been involved in any direct scandals. It appears to be about a 50/50 rate. The higher you go up on GC however, the more likely to be involved in at least something. 2000-2006 has an alarming amount of GC contenders whose names were either came up positive, or were involved in one scandal or another. Here's a glance at some names who have never been in any trouble I could find (in addition to those BroDeal, Zoncolon and myself already named):
David Arroyo, Sandy Casar, Evgeni Petrov, Marzio Bruseghin, Franco Pellizotti, Domenico Pozzovivo, Jurgen Van Den Broeck, Juan Manuel Gárate, Samuel Sanchez, Vladimir Karpets, Kim Kirchen, Mauricio Soler, Roman Kreuziger, Michael Rogers, Mikel Astarloza, Cyril Dessel, Tom Danielson.
Levi Leipheimer has actually kept his nose out of trouble, except he did have a positive test as an amateur that was overturned, and he followed Lance to Dr. Ferrari's office in 2000-2001. He now rides for the Hog, so I personally have a real hard time putting him on any "clean" list, though others might. This same rule applies to Yaroslav Popovych. In a similar way, I'd say the Schleck brothers fit into this paragraph as well. Papa visited Dr. Fuentes and gave him money, though neither Schleck brother was named in OP.