If the FBI didn't care enough to destroy drug related bitcoin they seized but instead chose to profit from a sale, they set a precident for similar future transactions whether they like it or not.
(1) The FBI did not held the auction to "profit" from it. They had in custody some valuable property (bitcoin) that, after the court declared the seizure legitimate, belonged by right to all the citizens of the US, equally. As such, the government could not destroy that property, and was morally bound to distribute it in some way to the citizens, or use it in their benefit, equally. So the government (not a particular agency) held an auction with the sole purpose of exchanging that property for an equivalent amount of dollars -- because dollars are much easier to spend in benefit of the people etc. than rolls royces, mansions in Alaska, frozen chicken livers, or bitcoins. The dollars will go to the Treasury, or perhaps to some specific agency, but always with the presumption that they are ultimately distributed to the citizens, normally in the form of public service.
(2) The coins were "dirty" (from the USG point of view) while they were in possession of SilkRoad/DPR, because they were the profit from illegal activity and could be used by a criminal organization or person. Once the coins were seized, they became the rightful possession of the people of the USA, in the government custody, so they obviously became "clean" at that point.
Likewise, banknotes stolen from a bank or paid for ransom are in principle "dirty", but if the police seizes them, or returns them to the rightful owner, of course they become "clean" again. Moreover, if a pizza parlor accepts a stolen banknote without being aware of its source, the banknote naturally becomes "clean" too; but no one else would know about that. This is basically why databases of "dirty" banknote numbers are perpetually out-of-date and have limited use.
(3) Stuff being "dirty" is distinct of it being "illegal". The cocaine sold by a drug peddler is an illegal substance, while the cash that he collects is only "dirty", and would remain dirty if passed on t o accomplices; but is obviously not "illegal stuff". The government is supposed to destroy illegal stuff, like drugs or explosives, because it has no legal way of converting it to dollars or using it for public good. On the other hand, cars and bitcoins can be legally owned and traded if they are "clean", therefore they can (must) be auctioned once seized, even though they were "dirty" before the seizure.