Our Gemara on Amud Aleph discusses three situations where prosecution of Beis Din can be suspended if the accusing parties choose to forgive their original charges:

אָמַר רַבִּי יֹאשִׁיָּה שְׁלֹשָׁה דְּבָרִים סָח לִי זְעֵירָא מֵאַנְשֵׁי יְרוּשָׁלַיִם בַּעַל שֶׁמָּחַל עַל קִינּוּיוֹ קִינּוּיוֹ מָחוּל וְזָקֵן מַמְרֵא שֶׁרָצוּ בֵּית דִּין לִמְחוֹל לוֹ מוֹחֲלִין לוֹ וּבֵן סוֹרֵר וּמוֹרֶה שֶׁרָצוּ אָבִיו וְאִמּוֹ לִמְחוֹל לוֹ מוֹחֲלִין לוֹ 

Rabbi Yoshiya says: Ze’eira, who was one of the men of Jerusalem, told me three matters: A husband who retracted his warning, his warning is retracted; and in the case of a rebellious Elder whom the court wishes to forgive, the court may forgive him; and in the case of a stubborn and rebellious son whose father and mother wish to forgive him for his sins, they may forgive him. 

וּכְשֶׁבָּאתִי אֵצֶל חֲבֵירַי שֶׁבַּדָּרוֹם עַל שְׁנַיִם הוֹדוּ לִי וְעַל זָקֵן מַמְרֵא לֹא הוֹדוּ לִי שֶׁלֹּא יִרְבּוּ מַחֲלוֹקֹת בְּיִשְׂרָאֵל 

And when I came to my colleagues in the South and told them these rulings, they agreed with me with regard to two of them, but with regard to forgiving a rebellious Elder they did not agree with me. They held that a rebellious Elder cannot be forgiven, in order that discord not proliferate among the Jewish people. 

In analyzing these three situations, we might find a common conceptual thread. All three have legal bases because of some future, or at least unrealized, behavior. The clearest example is the Ben Sorer, whom Rashi (Devarim 21:18) says is prosecuted for his future behavior that he will end up becoming a bandit.  We also can see from our Gemara that the rogue elder is being prosecuted more for the potential of disarray and discord it will lead to in the future, as it says, “So as not to proliferate (halakhic) discord and anarchy amongst the Jewish people”. And in a certain sense, the Sotah at this point is merely accused of adultery, and we do not know if she actually committed adultery. The Sotah test is It is not for the crime of adultery per se, rather it is about somebody who potentially sinned by secreting herself with somebody whom she was forbidden to do so and adequately warned against.  

In any case, what I find most significant here is that despite these societal concerns, the final ruling is that both the husband and the parents can revoke their claim and forgive it, thereby avoiding legal proceedings. Nevertheless, when it comes to the rebellious judge, no such forgiveness is allowed. Why? Because it will lead to social and halakhic anarchy. We can live with juvenile delinquents, growing up and being let out, so to speak, with no bail, and we even can live with the idea that  promiscuity may be continuing unchecked, but we cannot live with disintegration of the halakhic order.  Halakhic society in the Torah IS society.  Halakha is not just about what Esrog is kosher, but about how people must conduct themselves to promote the well being of society. See Moreh Nevukkim (III:27) where he states:

The general object of the Law is twofold: the well-being of the soul, and the well-being of the body. The well-being of the soul is promoted by correct opinions communicated to the people according to their capacity. Some of these opinions are therefore imparted in a plain form, others allegorically: because certain opinions are in their plain form too strong for the capacity of the common people. The well-being of the body is established by a proper management of the relations in which we live one to another. This we can attain in two ways: first by removing all violence from our midst: that is to say, that we do not do every one as he pleases, desires, and is able to do; but every one of us does that which contributes towards the common welfare. Secondly, by teaching every one of us such good morals as must produce a good social state. Of these two objects, the one, the well-being of the soul, or the communication of correct opinions, comes undoubtedly first in rank, but the other, the well-being of the body, the government of the state, and the establishment of the best possible relations among men, is anterior in nature and time. The latter object is required first; it is also treated [in the Law] most carefully and most minutely, because the well-being of the soul can only be obtained after that of the body has been secured. For it has already been found that man has a double perfection: the first perfection is that of the body, and the second perfection is that of the soul. The first consists in the most healthy condition of his material relations, and this is only possible when man has all his wants supplied, as they arise; if he has his food, and other things needful for his body, e.g., shelter, bath, and the like. But one man alone cannot procure all this; it is impossible for a single man to obtain this comfort; it is only possible in society, since man, as is well known, is by nature social. 

This is reminiscent of what Rashi remarks (quoting Bereishis Rabbah 38) about the distinction between the Generation of the Flood versus the Generation of the Dispersal (Migdal Bavel):

Which sin was greater: that of the generation of the Flood or that of the generation of the Dispersion? The former did not stretch forth their hands against God; the latter did stretch forth their hands against God to war against him (surely, then, the sin of the generation of the Dispersion was greater) and yet the former (the generation of the Flood) were drowned and these did not perish from the world! But the reason is that the generation of the Flood were violent robbers and there was strife among them, and therefore they were destroyed; but these conducted themselves in love and friendship, as it is said, “They were one people and had one language”. — You may learn from this how hateful to God is strife and how great is peace (Genesis Rabbah 38:6).

God can tolerate many sins so long as we all get along.