On some level doesn't the potential auction actually validate Bitcoins as a valuable asset that the Federal authorities seem relatively certain to have some reasonable future as a legal way of transferring value?
If the FBI had seized a warehouse full of worthless balls of lint...there wouldn't be any discussion of trying to auction them off...nor would that be the case if they were illegal drugs or weapons. It seems to me that their action in many ways validates that they believe whoever buys these are going to be purchasing at the very least a "commodity" of some degree of lasting value that the government anticipate they will ultimately be able to tax etc.
I do understand the concerns about potential market disruption (and there may be some degree of that albeit I would imagine briefly)...but even there I think there will be some sensitivity as to how this is done so as to maximize return for FBI (and the commissions of the potential auction house that will handle the deal)...not to mention a desire of the FBI to avoid headlines reading that the FBI has pocketed millions from sales to US citizens of a next day worthless commodity.