The consensus in Korea used to be that since this is a study of Western medicine, English (ie. terms used in America) should be the standard.
As you may already well know, most of Hangul comes from Chinese characters, and as such there WERE Hanja counterparts for every medical term in use.
With the coming of the hip Anti-Everything Age in Korea, though, things have made a turn for the ultranationalistic.
Use of Western medical terms seem to be frowned upon here, and even the original Hanja terms are beginning to be abolished (because they're from "짱깨." go figure). As a nod to our "brothers and sisters" in North Korea (who would like nothing more than to kill us, by the way), we now have ANOTHER version of medical terms, this time consisting of pure Hangul.
Let's use "glomerulonephritis" as an example. This term is also known as "사구체신염," but the current standard is "콩팥토리병." I'm not even sure if those are the exact words anymore.
Korean society has a really bad habit of having reason be overriden by blind emotion. Unforunately, this had to leak into our profession as well, and things have gotten pretty damn chaotic to say the least. That's what you get when you elect complete *****s to run the country. It's not easy to get top Honors when you're studying out of Harrison's and only a random pick of the two Hangul terms are ever used on exams.
Well, that used to be my excuse, anyways.