The title The Mysterious Benedict Society comes from the name the kids give themselves just before heading to the Institute on their mission to save the world (9.66). They choose this name for their crew—or rather, Constance chooses this name for the crew, and the rest of the kids agree to it—in honor of Mr. Benedict, who is, after all, the person who brought them all together. And since the book is about their adventures as they go undercover at L.I.V.E., it makes sense that their chosen team name should also be the title of the book.
Now the name Benedict comes from the late Latin name Benedictus, which means blessed, and considering how deliberate Trenton Lee Stewart was with many of the other names in the book, it's possible he picked Mr. Benedict's name for that reason. Mr. B is certainly blessed with above average intelligence, and the kids, operating under the MBS name do seem blessed in pulling off some of the capers they do over the course of the book. But The Mysterious Blessed Society? Not such a great title. If Stewart was making that connection at all, we're glad he stuck with Benedict.