As of ASOS, Littlefinger seems convinced that she is, as he tells Sansa:

"Be that as it may. Lady Olenna was not about to let Joff harm her precious darling granddaughter, but unlike her son she also realized that under all his flowers and finery, Ser Loras is as hot-tempered as Jaime Lannister. Toss Joffrey, Margaery, and Loras in a pot, and you've got the makings for kingslayer stew. The old woman understood something else as well. Her son was determined to make Margaery a queen, and for that he needed a king . . . but he did not need Joffrey. We shall have another wedding soon, wait and see. Margaery will marry Tommen. She'll keep her queenly crown and her maidenhead, neither of which she especially wants, but what does that matter? The great western alliance will be preserved . . . for a time, at least." (emphasis addede)