Prescribing based on Kingdoms is too close for comfort to the doctrine of signatures.
Doctrine of signatures is an idea that a remedy source will tell you what diseases it can treat. For example, a plant that has yellow flowers will treat liver issues. This kind of thinking is common in folk medicines, and especially in Christian and Muslim traditions; in traditionally Muslim or Christian nations, folk healers believed Allah/God deliberately made plants look like the parts of the body the plant could heal.
This idea has often proved useful in folk medicine, however it has no place in homeopathy. Homeopathy, as stated before, is matching a proving symptom to the symptom of the patient. Where the remedy is derived from has no implications for its prescription. Prescribing based on which kingdom the remedy comes from or where the remedy comes from in the periodic table directly implies that a remedy's source can tell us its use. For example: a mineral is structured, therefore the person who needs a remedy prepared from a mineral will have structural issues. This is a vast generalization, and there are many exceptions to such generalizations:
Phosphorus, a remedy made from the mineral phosphorus, produces symptoms of incredible sensitivity and hypersexuality, but sensitivity is associated with plants and hypersexuality is associated with animals. Hyoscyamus niger (a plant) produces some of the most intense sexual mania seen in the materia medica. However hypersexuality is, again, supposedly, a symptom associated with the "animal" symptom. The classic example of a "split in two" personality (a symptom associated with animals) is Anacardium orientale, another plant remedy. Even generalizing based on plant families can lead us astray. The solanaceae family includes the highly poisonous Datura stramonium, Atropa belladonna, (both lethal in small doses) but also potatoes, eggplants and tomatoes. Attempting to generalize based on remedy source will filter the remedies into artificial categories that can easily confuse a remedy prescription.
Hahnemann in Essay on a New Principle (Hahnemann's Lesser Writings, page 249) explains that we cannot generalize based on the remedy's origins (although such connections can be useful in memorizing), but rather we must pay attention to the proving symptoms in determining prescriptions.
Generalizing in this way is detrimental in another way: it's a generalization. My interpretation of the people I meet in the field of alternative health, and homeopathy especially, is that they want a repose from the de-humanizing categorizations and disease labels given to patients by the conventional medical profession. One of the virtues of homeopathy, supposedly, is that it is the only system of medicine that does not categorize people but keeps them as true individuals. This is different from Ayurveda and TCM, which also put people into the categories of "spleen qi deficient" or "vata". If homeopathy puts its patients into these kingdom and miasm boxes, are we not doing exactly the same thing?
Additionally, the definition of homeopathy matching patient symptoms (this does not include normal attributes of your personality) with the symptoms that arose from a proving. Note that in this process, there is no theorizing about the patient nor about the remedy; the process is a simple matching of one set of facts to another set of facts. If we match patient attributes to kingdom traits, we are in fact not practicing homeopathy.