(1) Torley says that ID is compatible with the view "that living organisms have built-in ends, and that their biological functions are inherent to them." But he goes on to say:
The point that Professor Dembski was making in The Design Revolution was simply this: that the inherent tendencies which define living organisms and make them what they are, do not in any way explain how the first living organism came to be. To explain this occurrence, an act of external agency is required: in other words, a Designer who created the first life. Neither chance nor the laws of nature can explain the emergence of life, because they are unable to generate the functional complex specified information which characterizes life.
This means that living organisms do not have inherent ends qua living, because it is the claim that the ends that characterize life must be imposed by an act of external agency independent of the laws by which the natures organized into living organisms act. This is to say that life is an artificial form rather than a natural form; and artifical forms are accidental forms rather than substantial forms. Thus the biological functions are only inherent to an organism in the sense that shape is inherent to a sculpture, or a particular interrelationship of springs and gears and pendulum is inherent to a clock. That is, it has them; but there is nothing here that actually counts as entelechy in the way an Aristotelian would understand it.
(2) Torley seems to confuse intentio in the Fifth Way with 'aboutness' and claims that the Fifth Way suggests that laws of nature are 'prescriptive' rather than just 'descriptive'. But this is not at all right. Intentio in the Fifth Way means an order or disposition or orientation to something; the arrow is given an (extrinsic) intentio to a target by an archer, for instance. This does not mean that the arrow is given any 'aboutness'; the arrow is not about the target, it simply is disposed to have one effect (hitting the target) rather than some other effect. On a Thomistic view some intentio is necessary for there to be any causation at all. 'Laws' of nature are neither 'descriptive' nor 'prescriptive'; they aren't even properly laws at all. They are merely a metaphor for talking about order. On a Thomistic view, moreover, God gives intentio not merely extrinsically, but intrinsically: the disposing of natural is an act internal to the natural things. No extrinsic agency is required; to think that there is, is to confuse the natural with the preternatural.
(3) Obviously Thomas Aquinas holds that it is possible for God to do "something to natural things in a different way from that to which the course of nature is accustomed". Torley, quoting a passage in which Aquinas discusses this, says that these acts sound like the acts of an artificer to him. These acts are called miracles. It is precisely the point, which Torley does not see, that the sort of conflation of ideas Torley is suggesting would, if taken seriously, commit an ID theorist to claiming that ID is the scientific study of miracles, and that its central thesis is that many biological systems were the results of divine miracles. (And Torley surely cannot have failed to realize that this passage was about miracles, because the very next sentence in the book, the first sentence of the next chapter, is " Things that are at times divinely accomplished, apart from the generally established order in things, are customarily called miracles.") If ID wants to pretend to be a 'big tent' and a theory of natural science, it cannot read Aquinas here as positing anything like the same sort of intervention it posits; if this passage shows that a Thomist should be sympathetic to ID, it can only do so on the assumption that ID forfeits its claim to be doing anything other than claiming the occurrence of divine miracles. The only other option here is that any resemblance is purely superficial, and that the passage does not do what Torley claims.
(4) Throughout Torley continues to treat the analogy between art and nature as if it meant that there was no fundamental difference between the two [e.g., in how the quotations from Aquinas are used]. It is precisely this conflation that makes it impossible for there to be any real and lasting rapprochement between Thomism and ID.
(5) The ID advocates have repeatedly made the claim that ID is more accessible than Thomism. This may be true; as I said before, since it conflates everything with everything else there's less to keep track of. But to claim, as Torley does, that ID presents "an argument which is evident to most people and that practically anyone can grasp, even if their philosophical background is very limited" is blatantly false. Most people cannot follow the mathematical ideas Dembski with barely any explanation throws left and right in, say, No Free Lunch; even allowing that Dembski's argument is flawless, it's not an argument "evident to most people". What is evident to most people, due to their religious beliefs, is that things were created by God, and what most people simply assume, given what little bits and pieces they take away from ID explanations of the arguments, is that this is what ID theorists are really arguing for, even if not precisely under that description. The ease of acceptance is not based on any ease of understanding; most people simply do not understand the details of ID arguments (and surely any that do could put the same mental effort into understanding metaphysical arguments). The ease of acceptance is the ease of hitchhiking: they don't see any distinction between what ID describes and what their religion describes, and so ID gets past any suspicions they might otherwise have by blending in. It also fits with a number of metaphors and analogies that have come to be common in our society. This is a pretty standard sort of thing (e.g., most physicalists are physicalists not because they can follow any of the sophisticated physicalist arguments but because of a hodgepodge of associations and analogies), and so doesn't itself suggest any problems of ID. But the explanation for acceptance of ID is due to psychological association and sociological influence, not rational assessment.