It's important to remember that this is an index of suspicion for a specific point in time. Earning a 0 in 2011 doesn't mean that there was never any suspicion. Indeed there riders here who subsequently confessed to doping who have 1 and 0 ratings (Zabriskie, Barie, Hincapie). We don't know what the suspicion index was in later in 2012 or in 2010 and earlier. Indeed perhaps the reason that the former Disco/Postal riders were rated zeros in 2011 is because the UCI was comparing their performances to earlier times when their suspicion index was higher.
A low suspicion number in 2011 doesn't exonerate anyone (any more than a high index convicts someone), it is just a handicapping of doping probability based on evidence available to the compilers of the index. There may may be evidence that the compilers were not aware of. I note that Di Gregario was rated a 2 and was arrested at the 2012 TDF. The index sets the odds, but sometimes long shots come in.