From what I read, Milley could still be court-martialed, found guilty. He would still be guilty even if pardoned. His record would not be expunged of his crime. He probably would still lose his government pension.
A presidential pardon generally relieves the offender of all punishments, penalties, and disabilities that flow directly from the conviction and restores important rights lost including the right to vote and possess firearms.
Eligibility for a Pardon
To be eligible for a presidential pardon, a petitioner must usually wait at least five years after their federal conviction before applying. This waiting period is designed to give the petitioner a reasonable period of time to demonstrate that they can be a responsible, productive, and law-abiding citizen. The waiting period begins on the date the petitioner is released from confinement or, if no confinement was awarded, from the date of sentencing.
Petitioners must have also fully satisfied whatever sentence was imposed, including all probation, parole, or supervised release, before applying for a pardon. It is important to note that the waiting period begins after the petitioner is released from confinement for their most recent conviction, whether or not that is the offense for which pardon is sought. Petitioners may request a waiver of this waiting period requirement, though such waivers are rarely granted.
A presidential pardon does not, however, erase or expunge the record of a military conviction. Expungement is a judicial remedy, rarely granted by courts, and cannot be granted by the Department of Justice or by the President. Instead, both the federal conviction as well as the pardon would both appear on your record. Even if you are granted a pardon, you still have to disclose that you were convicted at court-martial but may also state that you were later pardoned for the offense.
Additionally, the pardon of a military court-martial conviction will not change the character of a military discharge (e.g. dishonorable or bad conduct). To request a change in their characterization of service, a veteran must still submit a petition to their respective board for correction of military/naval records.
Eligibility for a Pardon
To be eligible for a presidential pardon, a petitioner must usually wait at least five years after their federal conviction before applying. This waiting period is designed to give the petitioner a reasonable period of time to demonstrate that they can be a responsible, productive, and law-abiding citizen. The waiting period begins on the date the petitioner is released from confinement or, if no confinement was awarded, from the date of sentencing.
Petitioners must have also fully satisfied whatever sentence was imposed, including all probation, parole, or supervised release, before applying for a pardon. It is important to note that the waiting period begins after the petitioner is released from confinement for their most recent conviction, whether or not that is the offense for which pardon is sought. Petitioners may request a waiver of this waiting period requirement, though such waivers are rarely granted.