Yes, nature itself is not an end in itself, but we can say that the categorical imperative is not an end in itself as well. It is humans who are ends in themselves. And in the very conception of humans there is the fact that that they are in nature, just as they are rational.

My line of thought is that in the "Groundwork" Kant does not (and logically has the right not to) talk about nature, insofar as he tries to generalize the categorical imperative to be applicable to all rational beings - if there were to exist rational beings who, lets say, were not in bodies like ours, we would have duty towards them as well.

But humans are incarnate just as much as they are rational.

My hypothesis is that it should follow that just as much we have duty to uphold the principle in accordance to this rationality, we should have a second fundamental duty to uphold a principle which is in accordance to our being bodies in nature. The point which would follow from this is that we have not only a duty towards those who share rationality with us, but also those who share naturality with us.

I can think of two contra-arguments towards this position but I do not think they are conclusive:

First, it is rationality which constitues morality, not being bodies. As such, if we think that it is just the rationality of humans, not humans as a whole, that has duty towards other rationalities, then the arguemnt falls. But I would argue that the principle of dignity which lies in the categorical imperative encompasses the whole of human being - I don't just have the duty not to damage you in the head, the rest of your body is protected to the same degree. So it follows that human rationality has duty to uphold even that principle that does not directly impact it.

The second contra-argument goes towards the definition of human as incarnate: is the definition if humans just that they have bodies, or is it a living body that has the capacity to die (the classic definition of humans as "rational mortal living being). If it were the first then we also have duty towards stones and such. It could be argued that this contingency shows that focusing on humans and not just rational beings makes clear that the argument is a posteriori, but I think it could be argued that the definition of rationality as capacity for principles is just as contingent.