A metaphysical "hypothesis of intelligent design" explains nothing at all. It makes no falsifiable predictions, it explains nothing about the nuts and bolts of the universe's provenance, either in a scientific or philosophical sense, and alternative materialist explanations are, without exception, even when empirically empty, inherently simpler and more reasonable.
I disagree with Baggott over the state of theoretical physics - in the absence of decisive, novel experimental results by which they can navigate I don't see what else theorists are meant to do, and the idea that anyone is blithely "accepting" mathematical constructions like M-Theory is a strawman - even string theorists couch their most forceful arguments for its reality in multiple caveats. This seems like strawmandering on a book-length scale. But I can at least respect that he cares about what's true regardless of what that truth turns out to be, which is at the crux of the scientific method.
On the other hand, inserting teleological thinking into the gaps in modern physics, for no reason besides your own discomfort with the scientifically-revealed meaninglessness of the universe, is a neglect of your obvious intellect. The Discovery Institute is not in the slightest bit interested in scientific discovery if that discovery has atheistic, materialistic consequences. It is inimical with the scientific community, and the neutrality of the scientific method, for that reason. The Templeton Foundation is similarly pernicious, although less openly and obnoxiously so.
If theorists are at a dead-end(and the jury is certainly out on that, contrary to Baggott's belief) then the solution will come not from religious dogmatists mangling their scripture to fit nature's cubby holes, or from theologians vaporously waffling about 'the ground of all being' and 'science's gesture to the ineffable' - the solution will come from theory and empirical investigation, just as it has in every single case there has ever been since the beginning of civilisation. That is not an exaggeration. Theology and philosophy, as wonderful as they may be in asking interesting and deep questions, are not going to unify quantum mechanics and general relativity. They have made no discoveries about the real world in their entire history, for the basic epistemic reason that neither of them have a means of objectively arbitrating between two competing hypotheses. It is only the scientific method, and experiment, that can do this, and casuistic wishful thinking about intelligent design won't change this fact.
P.S. - Don't necessarily take this as an attack on you. It is an attack on all those institutions and organisations who want to skew the default position of the scientific community in one direction or another. If you support them, then yes, I am criticising you. If not, then I am not.