In all but one of the examples cited, this was acknowledged, deliberate policy of the government at many levels. Extraordinary rendition, imprisonment without charge, torture, drone strikes, all were known, approved of, and carried out with the assistance of many levels of the central government.
The only example there that can be reasonably cited as an aberration of the norm is the judge taking payoffs for heavy sentences - that's an example of one piece of the machine going rogue.
Sure, the US has done good during all this time as well, but the atrocities cited are not "exceptions", they are a core part of the American government of the past decade.