That's the really sad thing about Trek Lit. They took this very interesting organization, which had its pros and cons, and just turned it into this strawman evil organization that's only rivaled by Mass Effect's Cerberus in stupidly evil actions.
There was never anything the least bit ambiguous about Section 31. They were quite unambiguously the bad guys from Day One in the canon, and Treklit just reflects that. (There is nothing "pro" about an organization that routinely appoints itself judge, jury, and executioner, and which engages in mass murder and genocide.)
You want moral ambiguity? Treklit's take on Starfleet Intelligence is very morally ambiguous.