Bottom line: I wish the editors and writers would raise the bar a bit and not fall back on Section 31 -- which is what happened in ZSG.
Well, personally I'd be happy if we never saw another Section 31 story again, except perhaps for the tale of them finally being exposed and brought down once and for all. But I don't think ZSG was just gratuitously "falling back" on S31 as a plot trope. The idea was to pick up on threads from the DS9 novels. I was privy to some of the early discussions behind the Pact novels, and I don't recall Section 31 even coming up at that early stage; it was just logical to use Bashir as a focus character in a spy novel that also featured Ezri, because that was an opportunity to follow up on established DS9 character threads. But Section 31's interest in recruiting Bashir is also an established, ongoing DS9 thread, both in the show and in the novels. So it kinda stands to reason that if you're doing a novel about Bashir being involved in an intelligence mission, Section 31 would come into play. It's not a gratuitous use of the organization, but a logical extension of one of Bashir's established character threads.