How about this? Sinclair is the commanding officer of Babylon 5 and continues to be for the rest of the series. His ex-fiancee Catherine Sakai "died" during a planetary survey with her group when their freighter blew up prior to the beginning of the series. Sheridan takes the role of General Hague.
Valen's destiny is given to Sinclair and Delenn's son.
And the reason why the Earth-Minbari War ended is because Delenn ran a bio-scan on Sinclair in captivity out of some curiosity that called to her and he was identified as one of the destined parents of Valen mentioned in an ancient Minbari prophecy. It was said in that the prophecy that a human and a woman merged of two worlds will become united, paving the way for Valen's birth and the eventual fullfillment of his destiny to be the man Minbar knows him to be thousands of years ago. Only the highest members of the Religious Caste and the Warrior Caste know of the prophecy. The Warriors think it's a buch of crap but is forced to stand by it since it was clearly written in Valen's hand. And attached to the prophecy are samples of the man and the woman's DNA, which are to be used to identify the parents and set things into motion for their union. Delenn felt immense guilt after realizing that she nearly killed one of the destined parents and that's why she went along with the decision to stop the war before it goes too far. Because if they are to let Valen be born according to prophecy, they need to let the human race live along with Sinclair and allow enough time to pass by until he meet the woman merged of two worlds. At that time, Delenn didn't know that the woman was her.
It's because of this prophecy that the Minbari chose Sinclair to be the commanding officer of Babylon 5. Because with Delenn there, they could keep a close eye on him and protect him from danger that could hinder his role in Valen's birth.
I never did like that whole "we discovered Minbar souls in human" reason to the ending of the war. It just didn't feel right in the show. What you guys think?