Marguerite, Lady Blakeney, is indeed the character most changed by the events of the plot. Her status as the book's protagonist is further enhanced by the fact that she's the primary agent in propelling the action forward. She also faces the most obstacles. This is largely because she's called upon at every turn to reconcile the two sides of her personality. On the one hand she's a Frenchwoman, and in her native country she took revenge on the Marquis de St. Cyr, inadvertently leading to his execution by guillotine, along with his sons. At the same time, she lives in England, married to an Englishman by the name of Sir Percy Blakeney, who unbeknownst to her, is none other than The Scarlet Pimpernel himself.
As the story progresses, Marguerite becomes more English and less French, leaving behind her tumultuous past to settle into the life of a devoted, loving wife. One can interpret this change as a mordant commentary on the respective political systems of the two countries: Revolutionary France, with its violence, tyranny, and chronic social upheaval; and England with its rule of law, rigid social hierarchy, and general stability.