For me, Section 31 was a risky thing to introduce. On the one hand, it made sense for a quick 'dark' fix in terms of added story potential in DS9 (especially during the Dominion War), and I loved the episodes with Sloan. But it's also a very easy thing to exploit, and something that could be used to turn Star Trek into something it's not - and I wouldn't just use Into Darkness as an example of that, I'd use those Enterprise episodes as well. It's not that I don't believe they'd exist (of course they would), it's just that it's something that I feel should only be used very, very rarely.
Imagine how different Chain of Command would've been if Section 31 had been introduced beforehand - Picard would have never been sent on that mission, Jellico probably would've been a member of them, and there probably would've been some back room dealing with the Obsidian Order. I'm not saying that wouldn't have been good, but the story didn't need it.
Anyway, I could go on and on, so I won't: I'll just say that even though I like it, it shouldn't be abused.
Regards the whole specialist team aspect, starships carry a big compliment of security personnel and I like to believe that they're trained a lot better than present day elite squads (SEAL, SAS etc). Therefore, I don't think they should make a huge song and dance around them. That's the role of the security officer.