She ordered everyone on the plane killed except for Coulson because "he's mine". If after that you still think it might not be her, then I don't know what to tell you.
Welp, when I'm wrong, I'm wrong. And I was wrong here.
Concerning Hand, she DID think Coulson was Hydra, so there was a little something to that. I didn't have Garrett pegged as the Clairvoyant until they were at the Hub and he was overly insistent on taking out Hand. That was when I figured it out.
I didn't see Ward's heel turn coming until he asked to personally lock away Garrett. Although, I think he will eventually turn face again because of his feelings for Skye and his emotional struggle over doing the right thing. The way he was zoning out at the end of the ep makes me think this.
I think it'll probably be minimal, just the same as with Thor 2. The only way I think it might affect the show is it might make Fury inaccessible to answer Coulson's questions because of what might happen to him in the movie.
Annnnd wrong again. Thor 2 had very little impact on the show. Cap 2 had a HUGE impact on the show.
I'll be interested to see how long it is before Coulson finds out Fury is alive. My guess is that Fury stays off the grid until the events of Avengers 2. Considering when the show airs, that would be around the time of the end of S2. Since the S1 season finale is airing May 13th and Avengers 2 is coming out May 1st 2015, we might end up with 2-3 eps at the end of S2 that deals with the fallout from the movie.
If you have seen The Winter Soldier, it's more then Clear: the Events in the Movie will have an Major Impact on the Series. Can't tell More on this Point without Spoiling it...
Agents of SHIELD has really hit it's stride. All of my previous complaints about the series have been washed away. Something from the films having this big of an effect on the show is a very good thing for it in the long run. I'm really glad I stuck with this show through the rough patches early on because it has gotten very good as of late.