Now, let's really think about this situation. Margaery has orchestrated a situation where she gets to return to Tommen's side. She does not have to do a walk of atonement. She's in a position to "help" her brother, Loras, atone for his sins. She's even saved the Tyrell army from causing certain irrevocable harm. If they had truly intervened, the Tyrells would be a huge target for the Sparrows going forward.
It goes even deeper than that, though. Margaery is disassembling the Lannisters bit by bit. For opposing the Sparrows (and thereby the crown), Jaime loses his coveted position as a member of the King's Guard. Cersei's plan — along with whatever true intentions were behind it — has been completely undermined. Margaery's bond with Tommen is stronger than ever, and she's effectively pulled him just a little bit further away from Cersei.
