I would've been happier if the series just didn't have Ashi's redemption arc at all. I don't feel like she really added much other than something to be sad about in the end. Redemption arcs just don't work too well with completely new characters in a series, imo. The sisters of Aku could still be in there, but they'd just be 2-3 episodes' worth of torment for Jack as he comes to term with killing humans, like how they originally did it, the difference being that he kills all of them, even Ashi.
Jack would then be on the edge of suicide after finally dealing with all the sisters, but then he'd have the sword symbolically returned to him by someone like the ghost of the Scotsman and his daughters, somebody who represents the thousands of people he's saved in the future, and why he can't give up now. Then have a finale battle similar to the one we saw, but with Jack actually pulling off killing Aku. With all the portals gone, Jack's out of luck, but all of his friends gather him up and cheer anyway, their world saved. Show a quick time lapse of Jack dejected, but helping the newly formed rebel army restore order to the world and break down Aku's governments and organized systems of cruelty.
Throw in a goofy mad science scene with various scientists he'd previously saved experimenting with time portal technology at the end which implies there could be a happy ending for both timelines. BAM.