My opinion about the topic Section 31 hasn`t changed.
I think Section 31 started with the best intentions but got corrupted. How early that started hasn`t been revealed yet. I hope this will also be a topic in future Enterprise Relaunch novels. I can imagine that because Earth, Starfleet is a new power among technically more advanced species who also have much more experience dealing with space faring civilizations, things were going on behind the scenes that pushed Section 31 into greyer and greyer territory.
Of course Section 31 as it is “now” is an organization that has to be stopped but I think it is too easy to dismiss it automatically as a terrorist organization that is consisting of criminals. From what I have seen, the higher up you go in Section 31, the more you find people responsible for crimes I can`t excuse. But not all agents should be seen as criminals. Trip was not a criminal and I very much hope that won`t change in future Enterprise books. After reading “Rogue” (still my favourite Section 31 book), I wasn`t left with the impression that Zweller is a terrorist, a criminal either. I am sure, there are Section 31 agents who do good work and saved a lot of lives without stepping over a certain threshold. And there are also people who have been used, misled, forced and blackmailed.
We know that there is a certain office or department of Starfleet Intelligence Admiral Nechayev is in charge of. What is going on here is often highly questionable, too, although I would like to think that even that SI department would never do certain things Section 31 did. On the other hand SI is accountable but having said that, I wonder how much the regular SI knows from what goes on in the darker areas.
Nevertheless, Section 31 needs to be exposed, preferably in a way that prevents the top heads to disappear or give them time to get rid of evidence that would convict them. I think each and every agent or person who otherwise worked for Section 31 should be seen as an individual case. I am sure, some of the agents Section 31 has could be extremely valuable assets for SI.