While I'm inclined to agree that
- it's wrong to use a natural human system (body part, aspect of the soul, naturally grounded activity, etc.) contrary to one of its natural purposes,
- it's wrong to use a natural human system in a way that isn't contrary to any of its natural purposes, but is also not in accord with any of its natural purposes.
I've been thinking about (2) today, and thought of an argument in favor of it. The human person is a closely unified whole (I actually do not think the human person has any actual proper parts). To use a part is to use the whole in respect of that system. Likewise, the telos of the system is a telos of the whole in respect of that system. Thus, to use one's system in a way that is not in accord with any telos that it has is to use oneself as a mere means, unless somehow one can create a new telos for one's own natural systems. Therefore if we keep the Kantian thesis that we shouldn't use ourselves as mere means, and supplement it with the metaphysical thesis that we cannot create a new telos for a natural system (this thesis seems anti-Kantian in spirit, but I think the historical Kant might well be friendly to it, given the Natural Law components in his ethics—say, his discussion of euthanasia or the solitary vice), we have an argument for (2). This would be a Kantian theory with a significant injection of Natural Law. Perhaps this kind of injection of Natural Law also helps with the problem of Kantianism being too formal to apply to concrete situations.
I wonder if (2) could be defended in the case of non-human natural systems. On the face of it, not: after all, it's perfectly acceptable to ride a horse, and carrying a burden doesn't seem to be a natural telos of its back. But I am inclined to think that it may be a telos of every non-human living creature on earth to serve human beings (maybe with some proportionality constraint built in). That may be why we may kill and eat at least some of them (it's uncontroversial that we may kill and eat edible plants and fungi). If this is right, then if one uses an animal for a purpose that is not a good, say by riding out on a horse to an unjust war, one not only does wrong by pursuing something that isn't a good, but one also does wrong by misusing the animal.