One of the greatest acts of sleight of hand involved with telling any ongoing narrative, whether it's a TV show or a comic book or a movie franchise, is giving the impression that you are creating major permanent changes in the story without burning down all the things that drew the audience to the thing in the first place.
When you've got a show like "Marvel's Agents Of S.H.I.E.L.D.," that's not a danger because this entire season has been a struggle for the show to find its voice and build a narrative head of steam, and any adjustments they make right now can only work to the show's advantage. It helps that last week's episode and this week's are both directly tied to the events of "Captain America: The Winter Soldier," since the film definitely shook up the status quo of the Marvel Movie Universe.
Of course, you can't just shake things up for the sake of doing so, either. That's no better than simply telling the same dull story without any adjustments. For it to really work, major changes have to offer something thematically important to the story, or they have to organically tie in to what's come before. It's a balancing act, and I don't envy the creative team behind "S.H.I.E.L.D." The pressure had to be monumental to get tonight's episode right, and it feels like they've finally paid off much of what they've been doing over the last sixteen hours of the series.