Here is Aquinas' judgment on such things.
In the infliction of punishment it is not the punishment itself that is the end in view, but its medicinal properties in checking sin; wherefore punishment partakes of the nature of justice, in so far as it checks sin. But if it is evident that the infliction of punishment will result in more numerous and more grievous sins being committed, the infliction of punishment will no longer be a part of justice. It is in this sense that Augustine is speaking, when, to wit, the excommunication of a few threatens to bring about the danger of a schism, for in that case it would be contrary to the truth of justice to pronounce excommunication (ST II-II Q43 A7 ad 1)....if the correction be omitted in order to avoid scandal, no spiritual good is foregone (ibid., ad 3).
In other words: punishment is intended for the sake of justice. But if the punishment will make things worse, then it becomes imprudent to inflict it - even unjust to do so. Seen in this light, the toleration shown by the Vatican (or less authorities) towards the wayward may be understood as forbearance for the sake of avoiding schism.
This is a reasonable perspective, it seems to me. I have heard others say this sort of thing (either George Weigel or Ralph McInerny, commenting on why the Church hasn't addressed dissent from Humanae Vitae more rigoroously): that the Church wants to avoid schism in some cases, which seems a likely consequence of too firm a disciplinary hand at times. Better, in this light, lovingly to attempt to reel in the wayward than to drive them off forever with harshness.
The connection of this with a recent post seems obvious to me. Toleration isn't necessarily weakness, as I (and others) may be prone to supposing, but rather charity in action. I suppose there may be something of a fine line: it would be possible to err on the side of being too lax. But there are risks on the other side as well - of being too much the martinet. Clearly there is matter for discretion and prudence here, so we armchair Inquisitors would be better off granting the benefit of the doubt.