Excellent point, it's definitely the context that matters. To me the article is arguing "code is not written in a vacuum" rather than literally "don't judge coders by their code."
This reminds me of the fundamental attribution error[1]. We tend to attribute the motivation behind our own behavior to context we are in, whereas we tend to attribute the behavior of others to internal characteristics.
I would make it part of the interview. Look at the code, think about it & ask the programmer about it. Reserve judgements until you have made an attempt to learn something about the context.
This reminds me of the fundamental attribution error[1]. We tend to attribute the motivation behind our own behavior to context we are in, whereas we tend to attribute the behavior of others to internal characteristics.
1. http://en.wikipedia.org/wiki/Fundamental_attribution_error