I will concede that the use of the word "slave" in the extra stanza is rather provocative in the context. However, I doubt if she meant the soul of time or of wrong (whatever they may be) to refer to slaveholders. The tone of the song as a whole, it seems to me, is not vengeful. In particular, I interpret the line

As ye deal with my contemners, so with you my grace shall deal

as alluding the parable of the sheep & goats (my contemners = the least of [my brothers]) and perhaps anticipating the peroration of Lincoln's second inaugural.

As for changing "die" to "live", that is no doubt more uplifting for present-day congregations, but it yanks the song out of its context, which is, after all, a war. The line after that one,

Let the Hero, born of woman, crush the serpent with his heel,

identifies Christ & the Union soldiers, and (I hope) the serpent with slavery, not the slaveholders -- it is the institution that tempts us to evil.