Interesting. I think that the confusion arises because the Microsoft paper was many people's first exposure to the term, which led people to assume that they had coined the term. Based on the Wikipedia article, it looks like it is a relatively new term, with the first usage I could find in 2011, but that it does predate the Microsoft paper.
It looks like Dan Eckert coined the term for this video: https://vimeo.com/19441262 then later used it to refer to the general technique, for which he registered http://www.hyperlapse.com/ in 2012. Other people started using it, like https://vimeo.com/50238512, and now Microsoft and Facebook are both developing applications that both use the term to automatically create hyperlapse sequences.
It looks like Dan Eckert coined the term for this video: https://vimeo.com/19441262 then later used it to refer to the general technique, for which he registered http://www.hyperlapse.com/ in 2012. Other people started using it, like https://vimeo.com/50238512, and now Microsoft and Facebook are both developing applications that both use the term to automatically create hyperlapse sequences.