Yes, the events of the second Thor movie take place after the events of The Avengers. But that may have been planned well in advance.
This wasn't always the case. Historically, Marvel has had different licensing deals set up at different studios: X-Men and Fantastic Four with Fox; Spiderman with Sony; etc. When it set about creating the Avengers initiative, it realized the logistical benefits of keeping everything under one roof. The Disney acquisition helped with that. The company still does projects under the terms of its legacy deals (see: the Spiderman reboots still being made at Sony, presumably at Sony's request, to exercise and thus keep its deal active). But the magic seems to be happening with the more centrally coordinated projects, like Thor/Iron Man/Cpt America/SHIELD/Avengers.
For many reasons, it was one of the best moments in the series.
It does reference The Hulk in the context of the license to Universal. But Marvel regained the film rights in 2006 and Universal was just a distribution partner on Norton-Hulk. It was much more a Marvel Studios film than any sort of Universal-driven successor to Bana-Hulk.
Nor does it ever mention Agents of SHIELD by name. To omit the name after specifically discussing the TV appearance clauses is pretty poor form for a journalist, particularly one who dedicated so much ink to the "Universe" strategy.
But I guess facing Marvel's mis-steps just didn't fit a "Marvel is unstoppable" storyline.
However: If I had correctly identified that the piece was shoddy, rather than the journalist, wouldn't materially impact the points in my post. That's a nit.
Including Marvel's existing mis-steps would materially impact the points of an article recounting Marvel's lack of mis-steps. That is not a nit.