"Major characteristics of his job were the clean, well commented code
and the smart, yet often unorthodox solutions."
I don't see any way in which one could reasonably interpret this statement negatively. If the solutions were smart, then by itself obviously that's a good thing, whether or not they were orthodox. And if they were both smart and unorthodox, that's even better, because:
the fact that they were unorthodox shows that you came up with them independently rather than just regurgitate some smart but unoriginal idea that everyone is taught in freshman year;
the fact that they were unorthodox and smart means you are not only creative and think independently, but your independent thinking actually leads you to smart solutions that haven't been thought about by (many) others. What's not to like about someone who has such characteristics?! I think only in some crazy place like North Korea would this be considered a bad thing.
Finally, the use of the word "yet" can be either a subtle logical error on the part of the writer, or a reference to the (probably correct, IMO) fact that if a solution is unorthodox, statistically speaking it is likely to be less smart than an orthodox solution, since if the unorthodox solution were superior then there would be room for someone to popularize the unorthodox solution so that it would eventually become orthodox. In other words, a situation in which there is a smart yet unorthodox solution is a kind of "market failure", or an opportunity for "methodological arbitrage", and hence somewhat rare. With that said, such situations clearly exist, and any person who has the ability to discover and exploit them is in my opinion worthy of high praise.