The line has long puzzled readers. In context it is hard to avoid reading “my contemners” as referring to the Confederacy, who have rejected Christian values in taking up arms in defence of slavery. But then the line sets up a parallel between the Union’s treatment of the Confederacy and God’s treatment of the Union, which, if we read it as an allusion to Mark 11:25 or similar passages, as in the question, would seem to recommend that the Union treat the Confederacy with mercy. This is puzzling because the very next line recommends quite the opposite course:
Let the Hero, born of woman, crush the serpent with his heel
(This is a reference to Genesis 3:14–15, “And the Lord God said unto the serpent, … I will put enmity between thee and the woman, and between thy seed and her seed; it shall bruise thy head, and thou shalt bruise his heel.”)
Edward Snyder noted that the difficult line has the wording “so with you my grace shall deal” (not “so with you I shall deal”) and suggested the following interpretation:
This somewhat cryptic line proves to be anything but a recommendation for mercy, when taken in connection with what follows in line 11. The idea is perhaps this: “Punish without stint those who have scorned me, and I will pour out my grace on you without stint.” The concept grace is peculiarly prominent in the New Testament, but in the sense of free grace, given without bargaining and without reference to man’s deserts. Here, however, Mrs. Howe has a concept more in the mood of Old Testament—a “fiery gospel”.
Edward D. Snyder (1951). ‘The Biblical Background of the “Battle Hymn of the Republic”’. In The New England Quarterly 24:2, p. 236.
Some imprecision of wording is to be expected because of the speed with which Howe composed the song. In her memoir she relates how, after returning from a review of troops near Washington D.C. in late 1861, she awoke early the next morning and composed the song while waiting for the dawn:
To beguile the rather tedious drive, we sang from time to time snatches of the army songs so popular at that time, concluding, I think, with “John Brown’s body lies a-mouldering in the ground; His soul is marching on.” The soldiers seemed to like this, and answered back, “Good for you!” Mr. Clarke said, “Mrs. Howe, why do you not write some good words for that stirring tune?” I replied that I had often wished to do this, but had not as yet found in my mind any leading toward it.
I went to bed that night as usual, and slept, according to my wont, quite soundly. I awoke in the gray of the morning twilight; and as I lay waiting for the dawn, the long lines of the desired poem began to twine themselves in my mind. Having thought out all the stanzas, I said to myself, “I must get up and write these verses down, lest I fall asleep again and forget them.” So, with a sudden effort, I sprang out of bed, and found in the dimness an old stump of a pen which I remembered to have used the day before. I scrawled the verses almost without looking at the paper. I had learned to do this when, on previous occasions, attacks of versification had visited me in the night, and I feared to have recourse to a light lest I should wake the baby, who slept near me. I was always obliged to decipher my scrawl before another night should intervene, as it was only legible while the matter was fresh in my mind. At this time, having completed my writing, I returned to bed and fell asleep, saying to myself, “I like this better than most things that I have written.”
Julia Ward Howe (1899). Reminiscences, 1819–1899, pp. 274–275. New York: Houghton Mifflin.