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Medical terminology derives from Latin and Greek because in the Middle Ages, when modern English was first forming, those were the prestige languages used by the educated elite. It was useful for educated people from throughout Europe to be able to speak freely with one another no matter where they were from, and it was Latin and Greek that were adopted for this purpose.
In part, the use of Latin and Greek was because of the many classical texts written in Latin and Greek: since it was on these prestigious works that a proper Medieval education was built. But by that logic, Arabic would've been another good language, since it was the Arabs who preserved many of these texts and reintroduced them to the West. Sure enough, there *are* a number of Arabic-derived words used in medicine and science, including alkaline, average, chemistry, and natron (the medieval "Latin" word for sodium; and indeed, some say the word sodium is also Arabic-derived). Ultimately, the continued use of Latin and Greek has as much to do with the fact that the Roman Empire still had two very important vestiges that remained powerful in Europe at that time: 1.) the Byzantine or Eastern-Roman Empire, an actual political entity; and 2.) the Roman Catholic Church, which (contrary to the reputation it gained later) sponsored Europe's first universities through its cathedrals, preserved literacy in its monasteries, and facilitated the re-importing of the Western canon back to Europe. Pope Sylvester II was particularly important in this regard.
In any case, the use of a prestige language for specialized vocabulary is perfectly normal. A similar thing is happening today with English in many cultures of the world; when a language lacks words for the minutiae of Western medicine, their doctors will often simply adopt the words of the doctors they've learned from... many of the same words that English once received/adopted/reinvented out of the Latin and the Greek.
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