I have to take issue with your assertion that a novel has a single "universal theme." In reality I think that every work of literature possesses a number of different themes that are open to interpretation and discussion, and this great novel is no exception, focussing as it does on one woman's journey to self-acceptance and maturity in a very interesting historical context. You might find it better to ask what it is that you yourself took from reading this novel. What message did you receive?
For me, this novel speaks a lot about religion. Clearly, the strict and kill-joy nature of Puritan religion is contrasted throughout the novel with the rather different approach that Hannah Tupper takes to religion and the way that she, and other characters such as Kit and Nat, experience religion through nature. Again and again reference is made to the particularly joyless nature of Puritan religion with its obsession on appearance and duty. This is contrasted with the way that Kit experiences nature in a religious fashion, most clearly identified in the Meadow and the way that it is linked to Hannah. Consider the following passage:
Perhaps she slept a little, but presently she opened her eyes and became aware of the smell of the warm earth and the rough grass against her face. She rolled over and stretched, blinking up at the blue sky. The tips of the long grasses swished gently in the breeze. The hot sun pressed down on her so that her body felt light and empty. Slowly, the meadow began to fulfil its promise.
Nature, here embodied in the Meadows that Kit has fled to, is explicitly described in terms that are reminiscent of transcendentalism. Kit seems to be able to find spiritual refreshment from the natural world that is described, from Kit's viewpoint, throughout the novel. The author thus seems to be pointing towards a more rounded approach to religion, rather than just focussing on the rules and regulations that dominated Puritanism, arguing for a gentler and more reasoned approach, as characterised by the welcoming nature of Hannah Tupper's home and the healing that characters find there.