Stanza 6 Summary

Get out the microscope, because we’re going through this poem line-by-line.

"Bring them down from their ruddy gallows;

All right, pipe down, Shmoopers. The soul's yakking again. We can tell by the quotation marks.
The souls telling someone or something to bring them (who?) down from "ruddy gallows."
A gallows is a structure used for hanging people. Ruddy means reddish. The "them" is presumably the humans.
This seems a little scary, but the soul is speaking figuratively…again. In other words, the humans aren't actually all hanging from gallows about to be hanged. The soul means something else, but it's hard to tell exactly what.
If gallows are usually reserved for criminals, maybe the soul, seeing humans as flawed, says "bring them down" as a way of accepting their flaws. All right, all right, don't hang these poor guys just for being human, the soul says.
This line reads like a resigned concession, as if the soul has accepted the fact that the day will start, no matter what, so it might as well make the best of it.

Let there be clean linen for the backs of thieves;

Here comes that prayer or wish again. This time, instead of wishing only for laundry, the soul wants to put that laundry to use—on the backs of thieves.
Again, we're betting this is figurative. We haven't really seen any thieves in the poem, but the soul is speaking generally of humankind, particularly about its flaws.
Sounds like the souls in a pretty accepting mood—generous, even.

Let lovers go fresh and sweet to be undone,

The soul hopes that when the lovers go off to have sex, they'll be dressed in clean, fresh clothes, like the criminals.
The speaker seems to be setting up a contrast between the impureness of human actions—sex and thievery—with the clean, fresh, angelic laundry.
It's as if the soul says, hey, if humans are gonna go be humans, they should at least be wearing clean clothes.

And the heaviest nuns walk in pure floating
Of dark habits,

The soul wants the burdened nuns to "walk in pure floating," which probably means in a more carefree, relaxed way. What's weighing these nuns down? Maybe it's the sins of the people whom they serve. Then again, maybe they're just a bit pudgy.
Either way, it's worth noting that this line has another contrast in it—between heaviness and floating.
"Dark habits" is a pretty clever pun. At first glance it seems like Wilbur means bad habits, but remember that a habit is what a nun wears on her head—maybe even making her literally heavier.

keeping their difficult balance.

We suspected something was up with all those opposites and contrasts in the previous lines of this final stanza.
Now we see that the soul accepts, understands, and maybe even loves humans for their balance of the good and the flawed.
For most of the poem, the soul elevates the spirits and demeans the humans, but toward the end we see things start to even out more.
The poem ends on a slightly positive note. The soul observes the noble struggle for humans to find balance between their flawed nature and their desire to be good.
It ain't easy being human, and the soul totally gets it. It's even cool with it, to boot.