Well, the way I see it, the movie's side has not acknowledged S.H.I.E.L.D. ever since The Winter Soldier (apparently the black suit Spider-Man wears was made by S.H.I.E.L.D., but there is nothing to indicate that), same with Coulson being alive. Granted, for the latter, no one else knew he was alive, when he was, but surely everyone knows S.H.I.E.L.D. is back, right? Well, sadly the movies aren't as willing to reference the tv side, but the tv side is always working off of the movies.
So, what I believe will happen is AoS will end with S.H.I.E.L.D. no longer existing, for whatever reason in the show, but the outside reason is because the MCU can't have S.H.I.E.L.D. still exist but not be used anywhere, with the show finished, and no way for them just to appear in the movie, because the assumption that people only watch the movies and would have no idea.
And, also because they no longer have a S.H.I.E.L.D. (both in the movies and in the MCU in general), that's why they're doing S.W.O.R.D. now. And maybe AoS will lead into S.W.O.R.D., so that when it appears in the movies, everything that is from the show can come over to the movies because the way it'll be handled in the movies is that they created it, and Daisy Johnson will be making her debut with this new organisation (which actually was set up in the show).
I don't know if that made sense. I kind of wrote it as it was coming to me. Essentially, AoS will end with the formation of S.W.O.R.D., however, the actual "formation" will be in the movies, so they can bring in the characters, but make it seem like this is their first appearance, rather than bringing them all in as S.H.I.E.L.D. agents and having movie-only fans having no clue what's happening.