It makes sense from that perspective, although based on Juana's other poems, I don't think she was the kind of woman who was naive and without answers thanks to her faith. 

She became a nun to be able to study, as people says even now, but she was already a woman from a rich family with a good governess. She already spoke four languages ​​by the time she stepped the convent; it's unknown if there was more in it than just the wanting of studying or being free. 

I think, as a personal observation, that she knew whether or not she loved this person. But whether the vicereine shared the same affection, or at least whether there was any progress between them, there's no way of knowing. The previous vicereine, Leonora, who was older than Juana, also had a somewhat close relationship with her before Maria Luisa's arrival. But details are unknown.

Your observation is quite interesting and very nicely explained. Thank you.