In the film, they present this possibility as something Pierce intuits might have happened, to which Steve replies that "if he knew Fury, he knows it's not true."



Then we see him use this to convince the council to immediately reactivate Project Insight, so one could say that the whole thing was fabricated to tarnish Fury's reputation.



But when they meet with Fury, we don't see him deny that he hired them, and as Natasha says, the whole operation was rather strange. So it wouldn't surprise me if Fury already suspected Project Insight and secretly orchestrated the kidnapping as an excuse to send Black Widow to steal the Lemurian's information.



This is Fury before he was flanderized, the same Fury who emotionally manipulated the Avengers into fighting Loki on Coulson's behalf.
A question that was left with me after rewatching Winter Soldier: so... did Fury hire Batroc to attack the Lemurian Star?