"Condemn" has another meaning as well:
to severely punish someone who has committed a crime, or to force
someone to suffer
(from Cambridge online dictionary)
This is the way "condemn" is meant in the sentence you are asking about. I guess it means that Unix is so important that not understanding it is almost like a crime, and if you commit that "crime", you will be forced to re-invent Unix yourself because it is so necessary.
FYI, I think this quote about Unix is referencing another famous quote, namely:
"Those who cannot remember the past are condemned to repeat it." **
** According to the Internet, G. Santayana originated that other quote, and in case you hadn't heard it, it might shed some light on the Unix quote.