This quote comes at the very end of the poem and reflects on the outcome of what happens when we nurse our grievances and hatred, just as the planting imagery used in the rest of the poem suggests. The first stanza of this poem presents us with two different and yet similar scenarios with very different outcomes. The speaker was angry at his friend, and told him about it, causing the death of his "wrath." The speaker was angry with his enemy, but did not talk to him about it and so his "wrath did grow" as a result. What happened as a result is that this hatred was left to grow and grow until it finally found its expression in the death of the speaker's enemy.
We are meant to read this poem allegorically and see how not expressing anger and pain is something that can result in hatred growing to such a massive extent that it causes us to do something that we regret afterwards and can result in death. The way in which the final two lines describe the speaker as being "glad" to see his dead enemy beneath the tree indicates that what has died is his own sense of moral decency through the way in which he has courted hatred and wrath to such a great extent.