From dictionary.com:

hy·poc·ri·sy   [hi-pok-ruh-see] –noun,plural-sies.

1. a pretense of having a virtuous character, moral or religious beliefs or principles, etc., that one does not really possess.

2. a pretense of having some desirable or publicly approved attitude.

3. an act or instance of hypocrisy.

I don't see how the author misuses the word "hypocrisy" at all. It appears to me that his case relates to #2 above - Jobs pretends to hold an attitude promoting open standards etc. when that is not the real motivation behind his actions at all.