There's no doubt in my mind that that status quo will be undone by the time Avengers 2 rolls around.
The tv series has to follow what happens in the movies, not vice versa. As far as movie watchers know, Coulson is dead and SHIELD is dismantled. They can't suddenly introduce back-to-life Phil Coulson, now director of a brand new SHIELD, in the movies without delving into some heavy backstory that no one has time for. So my guess is that by the time AoS concludes its second season, this new SHIELD will be gone as well. I also wouldn't be surprised if the show ends up building to Coulson dying again, just to maintain that "Coulson is dead" status within the movies.