[SPOILERS]
First, you have to take account that Sinclair/Valen double nature was an historical fact by then : Sinclair is destined to be discovered as a Minbari soul, and for that...some conflict is required, as Minbari are too isolationist to just study humans with the triangular-thingie.
Remember that EA was quite...not aggressive but arrogant. In spite of being warned by almost every contact they had to not go for Minbari, they disregarded and eventually went in a conflict because of this. If not incident because of Dukat's death, another incident would probably happen.
That said, it could be a lesser incident, and Minbari wouldn't go on a genocidal war (Am I the only one thinking they REALLY get it easy : I mean, they slaughtered whole populations, but it's fine? And Warrior Caste "We did nothing wrong" attitude without anyone just pointing out how weird it is to ally with someone that still denies that it was full of war crimes?) but more as "let's teach Humans a lesson, in order to prevent them rampaging in all the Galaxy Stilgar-way".
Of course, I'm partially using meta-thinking there : the war was doomed to happen in order for the past war with Shadows to make sense.