A presidential pardon may be granted at any time, however, and as when Ford pardoned Nixon, the pardoned person need not yet have been convicted or even formally charged with a crime. Clemency may also be granted without the filing of a formal request and even if the intended recipient has no desire to be pardoned. In the overwhelming majority of cases, however, the Pardon Attorney will consider only petitions from persons who have completed their sentences and, in addition, have demonstrated their ability to lead a responsible and productive life for a significant period after conviction or release from confinement.
It appears that a pardon can be rejected, and must be affirmatively accepted to be officially recognized by the courts. Acceptance also carries with it an admission of guilt.
It's that last part that's the gotcha. If Bush pardons some of his people for international lapses -- torture and other abuses of prisoners, etc -- then international courts could very easily use the pardon as evidence of guilt (it's an admission, yes?).