...But it is an interesting and entertaining moral argument and I feel it deserves to be had. The problem with Roddenberry's vision of a perfect future is that to depict it you have to brush a lot of problems under the rug and pretend they don't exist, and if Star Trek really is supposed to be a series that explores these moral themes then the Roddenberry Box is counter-productive to the supposed goal of the franchise. Right now in the real world there are organisations working for supposedly enlightened democracies that act in ways which are less than enlightened. How are we supposed to move past the need for these dark agents if we're not allowed to have a mature conversation about them?
Having Section 31 make plausible arguments is also important if they're going to be effective antagonists. I believe they are, for the most part, and it's largely because Sloan is permitted to hold his own against Bashir. Indeed, he even comes across as the more sophisticated of the two at times (given that Bashir can be rather black-and-white in his thinking). An effective villain needs to challenge the hero, and Sloan is permitted to do that; not only directly but by rebutting Bashir's idealized worldview for the audience. Sloan is the villain who offers temptation, who speaks what sounds reasonable, and that's the sort of danger we need in the antagonist if we're going to be addressing the issues Section 31 is concerned with. After all, if there weren't good arguments for such positions and behaviours, they wouldn't be so threatening and so it wouldn't be so important that they be challenged. Given that from this point on Sloan will be viewing Bashir as an asset whether Bashir likes it or not, a large part of his credibility as a villain consists of being able to construct a frighteningly good case for himself - just as this episode manages to construct a convincing case for Bashir being a programmed Dominion agent.