Was TWS clip at the end actually meant to be part of the episode? Putting this episode in context with the film?
Sort of. As was the bit after the meeting where Sitwell got orders to report to the Triskelion (since he's going to be in the movie). But it was also like the Avengers
trailer at the end of Captain America: The First Avenger
-- a mix of "continuation of the story" and "trailer for the next movie."