So, I'm not even an amateur writer, but here's how I would have ended the season:
Georgiou is sent along on her mission to blow up Qo'noS. The device isn't a ridiculous "hydro bomb" however. Let's keep the technobabble somewhat feasible, and say it's a dark energy weapon. When it goes off, it accelerates the cosmological constant in a localized area of space - essentially canceling the force of gravity and ripping the target planet apart.
The first half of the episode could go largely as it was shown originally, although hopefully with a little bit less hamminess by MU Georgiou. When Burnham finally goes down to the well/shrine thingy to confront MU Georgiou, she finds that she isn't willing to go along with the plan to turn over the bomb. Hand-to-hand combat ensues, and Burnham is ultimately forced to kill MU Georgiou. However, the bomb was not only keyed to her DNA, but her heartbeat, and the triggering mechanism goes off, albeit with enough time for Burnham to escape safely.
After we return to the Discovery, we get to see the destruction of Qo'noS in all its terrible glory. Word quickly comes in from Starfleet that the effort was a failure - the Klingon fleet decided that rather then return home and try and spacelift survivors, they were going to seek their vengeance on the Federation. Earth is bombarded from orbit, and billions die. Assaults on Andor, Vulcan, and Tellar begin. All hope appears to be lost.
Burnham says some line about their being no second chances in life. Stamets interjects that maybe there are some. Since the spore drive allowed them to travel forward in time, it should also allow them to travel back in time as well. The crew begins to hatch a plan, along with L'Rell, about how to undo the war, which has destroyed both the Federation and the homeworld of the Klingon Empire.
Discovery jumps back to just prior to the Battle of the Binary Stars. L'Rell has the shield/cloak frequencies of the Ship of the Dead. Burnham, Ash, and L'Rell use them to board T'Kumva's ship. L'Rell (and Ash) explain the outcome of the Klingon War - that T'Kumva's dream of a unified Klingon empire will die, Qo'noS will be a lifeless shell, and the houses will continue their petty squabbles. This convinces T'Kumva to reconsider - to try to unite Klingons from within, rather then through a show of force against the Federation.
However, not all of the Klingon houses are onboard with this idea. One faction - lead by Kol - still thinks they should attack the Federation fleet. A short-lived "civil war" breaks out among the Klingon houses, with Kor's forces destroying the Shenzou and all those aboard perishing. The battle also results in the "downtime" version of Voq dying - with Ash at his side, getting to see "himself" perish.
Ultimately though, T'Kumva and his allies succeed. As they were victorious in battle, T'Kumva is named the new chancellor of the Klingon Empire, and declares there will be a detente with the Federation...for now. Burnham gets to "save the day" but still feels bummed because she blew her chance to save "her" Georgiou. Stamets is thrilled to be in a world where Culber is still alive, but also feels weird, because he knows that Culber in this world still has his own Stamets. After the debriefing, PU Lorca walks up to Burnham, and says he hopes that in the future, she won't judge the things his counterpart did against him.
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