Philosophers, including some Christian philosophers, have maintained the basic principle that only the guilty deserve to be punished. Here is a sampling:
C. S. Lewis (The Humanitarian Theory of Punishment):
The Humanitarian theory removes from Punishment the concept of Desert. But the concept of Desert is the only connecting link between punishment and justice (emphasis added). It is only as deserved or undeserved that a sentence can be just or unjust. I do not here contend that the question ‘Is it deserved?’ is the only one we can reasonably ask about a punishment. We may very properly ask whether it is likely to deter others and to reform the criminal. But neither of these two last questions is a question about justice.
Martin Luther King, Jr. (A Comparison and Evaluation of the Theology of Luther with That of Calvin, 1953):
Concerning the work of Christ the two reformers stressed a substitutionary theory of atonement. They maintained that Christ actually took the place of sinners in the sight of God, and as a substitutee suffered the punishment that was due to men. But all of this is based on a false view of personality. Merit and guilt are not transferable from one person to another. They are inalienable from personality. Moreover, on moral grounds, a person cannot be punished in the place of another.
A. M. Quinton (On Punishment, reprinted in Philosophical Perspectives on Punishment, ed. Gertrude Ezorsky, pp. 6-15):
The essential contention of retributivism is that punishment is only justified by guilt. There is a certain compellingness about the repudiation of utilitarianism that this involves. We feel that whatever other considerations may he taken into account, the primary and indispensable matter is to establish the guilt of the person to be punished (p. 7).
For the necessity of not punishing the innocent is not moral but logical. It is not, as some retributivists think, that we may not punish the innocent and ought only to punish the guilty, but that we cannot punish the innocent and must only punish the guilty. Of course, the suffering or harm in which punishment consists can be and is inflicted on innocent people, but this is not punishment, it is judicial error or terrorism or, in Bradley's characteristically repellent phrase, "social surgery." The infliction of suffering on a person is only properly described as punishment if that person is guilty (p. 10).
Kurt Baier (Is Punishment Retributive?, reprinted in Ezorsky, pp. 16-24):
For 'punishment' is the name of a method, or system, of inflicting hardship, the aim of which is to hurt all and only those who are guilty of an offence. For this reason, a system of punishment requires a more or less elaborate apparatus for detecting those who are guilty and for allotting to them the hardship prescribed by the system (p. 18).
If, after the jury has found the accused 'not guilty', the judge says 'I sentence you to three years' hard labour', this is not just an unusual case of punishing the man who is innocent, but not a case of punishment at all. And here it would not only not be pedantic, let alone wrong, but perfectly right to say that this case was not a case of punishment. (p. 20)
Immanuel Kant(Justice and Punishment, reprinted in Ezorsky, pp. 102-06):
Juridical punishment can never be administered merely as a means for promoting another good, either with regard to the criminal himself or to civil society, but must in all cases be imposed only because the individual on whom it is inflicted has committed a crime. For one man ought never to be dealt with merely as a means subservient to the purpose of another . . . . He must first be found guilty and punishable, before there can be any thought of drawing from his punishment any benefit for himself or his fellow-citizens (pp. 103-04).
This debt which is original, or prior to all the good a man may do--this, and no more, is what we referred to in Book One as the radical evil in man--this debt can never be discharged by another person, so far as we can judge according to the justice of our human reason. For this is no transmissible liability which can be made over to another like a financial indebtedness (where it is all one to the creditor whether the debtor himself pays the debt or whether some one else pays it for him); rather is it the most personal of all debts, namely a debt of sins, which only the culprit can bear and which no innocent person can assume even though he be magnanimous enough to wish to take it upon himself for the sake of another (Religion within the Limits of Reason Alone, p. 66).
H. J. McCloskey A Non-Utilitarian Approach to Punishment, reprinted in Ezorsky, 119-34):
Punishment which we commonly consider to be just is punishment which is deserved. To be deserved, punishment must be of an offender who is guilty of an offence in the morally relevant sense of 'offence.' For instance, the punishing of a man known to be innocent of any crime shocks our moral consciousness and is seen as a grave injustice (pp. 120-21).
F. H. Bradley (The Vulgar Notion of Responsibility, reprinted in Ezorsky, pp. 109-10):
If there is any opinion to which the man of uncultivated morals is attached, it is the belief in the necessary connexion of punishment and guilt. Punishment is punishment, only where it is deserved. We pay the penalty, because we owe it, and for no other reason; and if punishment is inflicted for any other reason whatever than because it is merited by wrong, it is a gross immorality, an abominable crime, and not what it pretends to be. We may have regard for whatever considerations we please--our own convenience, the good of society, the benefit of the offender; we are fools and worse, if we fail to do so. Having once the right to punish, we may modify the punishment according to the useful and the pleasant; but these are external to the matter, they can not give us a right to punish and nothing can do that but criminal desert. This is not a subject to waste words over: if the fact of the vulgar view is not palpable to the reader, we have no hope, and no wish, to make it so (emphasis added) (p. 109).
I like the way Bradley phrases it. The idea that only the guilty deserves to be punished is so obvious and self-evident that its a waste of time to argue it with anyone who denies it. To quote what Paul told the Corinthians (in regard to another matter): But if any man be ignorant, let him be ignorant (1 Cor. 14:38, KJV).