Most of a director's work lies in getting good collaborators and working well with them. We know the names of auteur directors (as well as the take-charge ones like Cameron), but what they do is not required of the job description. Considering what we know of JGL's attitude about collaboration with HitRecord, I think he could do it and not go Shyamalan-on-a-big-budget with it. And in terms of directors making jumps from tiny budgets to big budget, not only Nolan did it, but the Wachowskis too. All the Ws were armed with was a powerful vision - they made Bound to prove they could direct at all, then they were off to the races. So it isn't the first time WB has taken a chance.
The worst that might happen is a well-intentioned misfire like Superman Returns (IMO), but hopefully with Gaiman involved, there's less chance of that happening.