There is technically a way to incorporate the concept you are trying to talk about; I gave you an upvote to undo the downvotes you are getting on this question.
There is a reason why there is a kneejerk reaction for the others to be downvoting your question. Under the wavefunction form of quantum mechanics, there is no way to incorporate the temperature. Temperatures are captured by classical mixtures, and in the wavefunction formalism, there is no way to talk about classical mixtures, only quantum superpositions. Another way of expressing this is that wavefunctions can only talk about pure states, and temperature is expressed by mixed states. As such, we have to first tell you that the thing you are looking for is not even expressible inside the standard form.
On top of that, most physicists would be aware of the fact that the nuclei's temperature is different from the electron's, sometimes dramatically so. For example, we know that there is the phenomenon of para- and ortho- states, e.g. in hydrogen gas and in oxygen gas. The spin of nuclei is the most experimentally visible part of nuclear physics, and yet even there, it easily can take days as the nuclei lags behind the electrons at thermal equilibriation. So, even if we take your concept at face-value, it is quite important to stress to you that the coupling between nuclei and electrons are weak enough that they can exist at different temperatures for really long times. I mean, if it is so weak that it takes millions of years to equilibriate, then for all intents and purposes you should consider them as never going to equilibriate, and have to deal with their separate temperatures as a fact of life. After all, as Feynman put in his little-known statistical mechanics textbook, what we are interested is an intermediately infinite amount of time, since, given really ridiculously long times, any gas will poke holes in their containers and exit.
The correct way to study this problem is to consider the density operator formalism. There are ways to "directly" get these things via some complicated Wick rotated path integral, and because it is Euclidean, it is actually better mathematically motivated than the usual path integral in Minkowski metric. Then you can talk about the nucleus having a temperature and also the electrons having a temperature, and even have them be the same temperature. Needless to say, the result is obvious: Basically for all the temperatures we care about in everyday life, the deviation from just assuming $T=0\,$K is negligible. This more than justifies why textbook treatments ignore the complication.
If we want to work purely with wavefunctions, that is also possible. Simply compute the ground state wavefunction and the first excited state, and compute the contribution of the first excited state's contribution to the density operator. It will be so small as to be irrelevant.
Of course, none of the above considerations will work in extreme conditions. For example, if we are considering a star, especially when we want to simulate a supernova, then we have to treat everything relativistically, including both the temperature and the pressures. The excited states will no longer be as negligible as they are in everyday life.
Now that I have outlined the way to consider what it is you wanted to consider, I would like to offer yet another reason to just stick with the simpler stuff. The nucleus is necessarily a dense soup of quarks and gluons. We talk about a temperature distribution for them, no problem. However, condensed matter physics tells us that the very fact of fermions being condensed, implies that there would be an equivalent huge Fermi temperature that we can define for them. This is exactly the same thing as in the sea of electrons in a metal, they essentially are at some $10000\,$K, such that room temperature is a tiny alteration on the big picture behaviour. It will barely be perceptible. So, really, just stop worrying about this.