Read the article. There's a quote.
'?Valve co-founder Gabe Newell and Star Trek director J.J. Abrams announced they are working on an unannounced game project together.? Newell also announced that he is investigating the possibility of working with Abrams on a Portal or Half-Life film.'
So Gabe and Abrams are working on something, and also discussing a Portal or Half-Life film. That means whatever they are working on is NOT a film for those franchises.
I'll admit I liked 2009 Star Trek, but how much stuff are we going to pile on JJA before actually letting him make these films? Another Star Trek, 3 Star Wars, Portal/Half Life, Mission Impossible, and I'm pretty sure he said he wanted to do a Cloverfields sequel or similar film.
EDIT: Regarding people talking about how the Portal one fits into the existing storyline... Why does it need to? The main focus is in the title, the PORTALS. If the film uses the portals as a foundation it can go anywhere from there and work successfully in my opinion (if done well of course)