Question

in the poem a slumber did my spirit seal how does the poet's beloved become an inseparable part of nature

Answer 1

Now that Lucy has died , she can neither hear nor see. She has been buried underground. She is merged with rocks and stones. She has become an integral part of nature. She is rolled down in earth's diurnal course.

Answer 2

It is the deep sleep 'closed off' his mind of soul. The beloved of the poet was dead. Also she was now not alive.

Also, the poet remembers that her beloved via this poem.  In fact, she turns into the integral part of the nature.  

Actually, she is   also rolled round in course of the earth with trees, rocks and stones.