"affected kidney" certainly does NOT translate to "Nierenerkrankung" (or "Nierenbefall"). While an "affected kidney" is a kidney, a "Nierenerkrankung" is a disease (Erkrankung).
I think your example is pretty good. Using LEO's translation, the sentence would read in German: "Der Chirurg sollte sorgfältig darauf achten, die Nierenerkrankung zu operieren, nicht die gesunde." (The surgeon should take great care to operate on the renal disease, not the healthy one.). Doesn't make too much sense, does it? :-)
To Un-affected writer:
You wrote: "With 'infected', all the given examples make sense."
Sorry, I have to disagree for 2 reasons.
Of course an infection of the kidney is a renal disease. But not every renal
disease is an infection -- there are several other kinds of renal diseases.
It might be of some interest look how the words "kidney", "renal" etc. are used in the world's most widely used general medical text: http://www.merck.com/mrkshared/mmanual/sectio...