In Sor Juana Ines de la Cruz's "Reply" ("Respuesta a Sor Filotea") to Sor Filotea de la Cruz (actually a bishop of Puebla writing in disguise), I do not feel that the tone changes, but that it remains constant.
Sor Juana's tone is informative rather than argumentative. She sounds quite humble as she gently defends a woman's right to study and share her opinions. She admits that people might, with good reason, find fault with her essays and/or letters. She invites (and expects) others to disagree, as she disagreed with Portuguese Jesuit, Father Antonio Vieira and a sermon he wrote in 1650, which seems to have started the difficulty in the first place—when she wrote critically about the sermon.
However, while Sor Juana is seemingly humble and deferential, one need not read too strenuously to "hear" what she seems to be saying between the lines. She notes a desire to be obedient when a mother superior ordered that Sor Juana should not read.
...I obeyed her (for the three months or so that her authority over us lasted) in that I did not pick up a book.
While Sor Juana never read a book during those three months, she could not force herself not to study and learn. Instead of having a book as a primer, nature became Sor Juana's classroom, and she studied the world around her...
...I studied all the things that God created, taking them for my letters, and for my book all the intricate structures of this world...
When Sor Juana writes about doing kitchen work (an "acceptable" way for a woman of the day to spend her time), it almost seems tongue-in-cheek. She asks Sor Filotea...
...what can we women know, save philosophies of the kitchen?
Because Sor Juana struggled for permission to learn to read and write at a young age, and rather than marrying, sought refuge in the Church as a nun where she could have certain intellectual freedoms, not for a moment do I believe that that Sor Juana felt a woman belonged mindlessly in a kitchen.
This line sounds almost sarcastic or subtlely patronizing. Sor Juana probably never did things half-heartedly. She may not have loved cooking, though I'm sure she applied herself—even though she would have preferred to write or read.
I sense that Sor Juana is doing all she can to placate and not offend. And while we may feel we can read between the lines and draw inferences about what she was referring to or how she felt, she had no desire to aggravate anyone, especially the men in positions of power within the Church and society. Her primary reason may have been to remove herself from the public eye (during a dangerous time to challenge religious doctrine) so she could do what she really wanted: learning, thinking, writing and growing intellectually.
So while I think there was a great deal going on beneath the surface of her letter, my sense is that Sor Juana worked hard to control any frustration that she might have felt in having to write such a letter, keeping the tone constant throughout.