I have to agree. The dishonesty in these two characters is a dishonesty against a flawed system, but not against a system of higher morality (in this case, God). Both men act out of a pureness of heart, which, in God's eyes, could be considered the epitome of honesty. The lies which are told, the hiding that takes place, the changing of names, etc., all of these things seem trite when observed against the bigger picture of "morality," especially when that morality has been identified with God.
Let me begin again; my post was obliterated when I edited.
Javert's honesty is a rigid adherence to the criminal justice system of his day: a set of accepted standards--a punitive, vengeful form of justice. The pursuance of Valjean by Javert is based upon this system that condemns Jean for taking bread to stave off the desperate hunger of his family. The flaw in Javert's truthfulness is that Valjean is not a true thief, an evil person. When Valjean rescues Javert from the revolutionaries, Javert cannot reconcile the goodness in Jean to the "truth" to which he has so rigidly pursued Valjean. It is this comprehension of the moral truth that, at times, reaches beyond the accepted standard which leads Javert to despair of the worth of his life and, thus, end it.
And, it is the knowledge of moral truths that the bishop recognizes and lives by. When he tells the gendarmes returning the candleholders to him that they are a present to Valjean, the bishop displays a morality that supercedes the standards of a society. For, he knows that Jean was unjustly imprisoned and unjustly prevented from obtaining work because of his yellow card of identification. The bishop, thus, influences a great struggle in Jean's heart between good and evil, a struggle that leads Valjean to moral redemption.
Hugo's morality is a morality of revolution against injustice, against the sophist "truths" of society that Javert represents. Hugo's Romantic belief in the intrinsic goodness of man reaches beyond the flawed laws of society. It is a higher truth, not one made by man.
An intriguing question! Maybe the problem with Javert's honesty is that the premise on which he bases his truth is flawed; it is sophism.