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Even if, as you argue, "Holder is no more tainted by his defense of Chiquita than lawyers who defend accused terrorists at Guantanamo are tainted by that" (and I think the analogy inappropriate and unconvincing), that doesn't mean he isn't compromised by it.
Dan Kovalik points to HRW's recommendations that the DoJ should
"[c]reate meaningful legal incentives for paramilitary leaders [a number of whom have already been extradited to the U.S.] to fully disclose information about atrocities and name all Colombian or foreign officials, business or individuals who may have facilitated their criminal activities," and "[c]ollaborate actively with the efforts of Colombian justice officials who are investigating paramilitary networks in Colombia by sharing relevant information possible and granting them access to paramilitary leaders in U.S. custody."
http://www.huffingtonpost.com/dan-kovalik/lawyer-for-chiquita-in-co_b_141919.html
And he suggests that there's now a question mark as to whether these recommendations will be acted upon if Holder is AG.
More importantly, the appointment sends a mixed signal from the new administration about its commitment to labour rights in Colombia and elsewhere.
The issue is not whether it was appropriate for Holder to take the Chiquita case, but whether it is appropriate for Obama to appoint someone who did take the case.