I think her transformation is less about a single book and more a mosaic built across several, with the most crucial probably being Timothy Zahn's 'The Last Command'. That's where we see the payoff, the final push from the Emperor's hardened agent to someone making her own choice. But focusing just on that misses the setup. 'Mara Jade: By the Emperor's Hand' (the comic and the prose adaptation) is essential for showing her state immediately post-Endor—lost, vengeful, still hearing the Emperor's command. It's raw survival, not yet transformation.
For the actual change, you need the 'Hand of Thrawn' duology, 'Specter of the Past' and 'Vision of the Future'. The early novels had her fighting the change, but here, years have passed. She's running a business, she's in a sort of truce with Luke, and the plot forces her to confront her past directly. The long conversations with Luke, the unraveling of the Thrawn clone mystery—it all peels away the layers of her Imperial conditioning. You watch her move from a smuggler with a past to a partner, and finally to someone who accepts a new role. The final decision she makes about the Emperor's last command in 'Vision of the Future' is the true endpoint of the arc, handled with a subtlety that the more action-packed earlier books couldn't manage.