Agreed. I read the article and it's... basically just trying to stir up panic over nothing.
NPAPI had a good run. It was made in 1995 and was used by Chrome, Internet Explorer, Netscape Navigator and Firefox, Opera and many other browsers (obviously not in that order). But it's been showing its age for a long time, and most browsers have dropped support for it years ago - Firefox keeps it alive purely because of Flash. But Flash is also implemented for the Pepper API, so if they can get enough of Pepper implemented to run Flash through that then they can finally ditch NPAPI. The alternative would be to invest a fortune inventing a whole new Mozilla-specific architecture just for Flash on Firefox and hope that Adobe still cares enough about both Flash and Firefox to reimplement the plugin for them - not likely.
Getting PDFium to work was the proof-of-concept for a minimal Pepper implementation on Firefox. Just enough Pepper API to run Flash is the end goal for now. Maybe they'll eventually decide to do a full Pepper implementation, but I don't think that's a concern for now.
This doesn't mean they plan to replace PDF.js with PDFium (which doesn't mean that they won't do so; I hope they don't, because PDF.js has been working very well for me and doesn't require any plugins)