Yes, she overstepped her boundaries. It should have been a team decision between Rohit and her. She needs to understand that she is no longer the sole player here. Rohit is equally affected by everything she does.
Having said that, I do feel that expecting her to keep a secret, to disregard her own opinion and thoughts is a monumental expectation, stressed further by the fact that she was not given the entire truth. Yes, Rohit is under no obligation to share all family secrets with her. But that holds true only as long as there is no expectation from his end to blindly aid him in his hide-and-seek game. The moment you include your wife in the ongoing decisions regarding anything big, she deserves to know the truth. If Sona was not expected to hold her silence or blindly go "with-the-flow" with the rest of the Sippys, then sure - Rohit doesn't need to share everything with her. But that is NOT the situation anymore.
My husband doesn't tell me everything about his family either, but if I am expected to behave a certain way in front of them or to not talk about something specific - I am always given the full picture as to why I am being expected to follow through. There is only so long a self-respecting person will nod and stay mum to everything around them unless they understand the gravity of the situation. I do not defend Sonakshi, but she's not the only one who is on the wrong side here.