I don't think we can use past simple here. It's not (in my opinion) a question of ambiguity. The reason is this: we're referring to a very specific "had done", which is "what he had done to solve this great problem". Therefore, "understand what he had done" allows the reader to immediately understand we are talking about the solution he devised, rather than achievements over the course of his lifetime (which is what the use of past simple implies).
As a standalone segment, your supposition (in the last part of your question) regarding:
Everyone wanted to understand what he did.
Is correct. I take this to mean "what he did (for a living)", which is obviously not what we want to echo in this case.
As a general observation about past perfect; this is the "strictest/most self-explanatory" tense in the English language in my opinion. I say this because it almost always goes hand in hand with a past simple giving reference to the order the two events occurred (the two events being the past simple one and the past perfect one), without having to use other elements of speech to qualify the order (though allowing for qualifying words to be used).
Here's an example of what I mean:
I finally got to wear the t-shirt I had made (some days before/earlier/etc).
The use of past perfect explicitly references the prior action without requiring further explanation.
I really feel this is the case with your example and so I conclude that "making it simpler" is counter-intuitive. It is already the plainest it could possibly be.