By commuting Libby's prison sentence only, and leaving intact the conviction and fine, Libby is still entitled to appeal his sentence and likely can assert the Fifth Amendment.
I haven't researched this but it seems unlikely he would appeal, and if he lets the period to appeal the sentence lapse (90 days ETA: 45 days after filing the notice) a 5th A claim on those grounds would leave him SOL. Still could claim it on the basis of some other prosecution though, which would make the commutation moot.