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While it does seem unlikely that attempting to prosecute Bush & Co. here in the US would prove fruitful, there are at least two possible useful results from an investigation, and even from a Bush pardon.
First, in retrospect, it would seem obvious that one serious flaw in the pardon power is its seeming grant of the power of self-pardon. It would seem reasonable to consider the passage of an Amendment barring the use of the pardon power by a sitting president to pardon either himself, or any member of his administration (current or former member). Even if future administrations feel pressured to grant pardons - if only to preserve the hope for themselves - this route, ala Nixon/Ford, still seems infinitely preferable than the idea that a President should have the unlimited ability to pardon himself. Should Bush choose to exercise a blanket pardon, one might at least find the impetus to pass such an amendment.
Lastly, an important point of an investigative committee, and undoubtedly a matter of some concern to members of the administration, is not their liability in the United States, but their potential foreign liability. Should an investigation reveal serious wrong doing, it is quite likely that individuals would (theoretically) face international liability for their actions. Note here in particular the recent historical indictments in England and Spain against Gen. Pinochet or former members of the Spanish fascist forces - it is certainly permissible under international law, and it is not unheard of for foreign courts to indict foreign officials. While it is unlikely that the United States would ever extradite a former official even if charged elsewhere, the mere possibility of future charges or extradition, or the actual bringing of charges - which would likely serve as an effective bar to foreign travel for the indicted individuals, lest a foreign country detain and extradite them to the prosecuting country - would certainly be a significant weight for former officials in and of itself.
As such, the unlikely nature of US prosecutions does not negate the usefulness of an open investigation, nor is a blanket pardon a guaranteed escape ticket for administration officials.