You're right, it is poetic. I don't really understand the symbolism either, but I can at least help with the meaning.
The full verse is:
Sorrow has a human heart
From my god it will depart
Which can be rewritten as a compound sentence like so:
Sorrow has a human heart; from my god it will depart.
Since semicolons are the same thing as ", and" or ", but" let's swap that out:
Sorrow has a human heart, and from my god it will depart.
Word order here is still weird. Let's fix that, too:
Sorrow has a human heart, and it will depart from my god.
Aha! Now we can see that the "it" in the part you're asking about is referring specifically to "sorrow" from the previous line. "Sorrow will depart from my god."
I won't attempt to deconstruct the symbolism here, but I hope this helps anyway.