'A large amount of gun powder exploding' wouldn't realistically be able to take out most of the population of Europe, or lead to gunpowder being banned by multiple nations, etc, either.
I'd find it far more believable for gunpowder just to have never been invented or never become a thing of widespread use in warfare than to have it all come down to one specific incident, with every single country having the exact same reaction to that incident. All it would take is Genghis and his armies being a little more inclined to slaughter everyone when conquering China, or the relatively small number of people who knew how to make it not being able to pass it on or their writings being lost...really any variety of things can stifle a technology or an idea and lead to it catching on or not, and not always the dramatically obvious.
If the plot isn't specifically about Genghis Khan or Alexander the Great it probably won't be necessary to go into this kind of detail about the setting's history in the story itself anyhow. If you establish that gunpowder was a late invention and weapons technology either developed slowly or took a different track in this world, readers aren't going to need an elaborate explanation as to why to accept that.
The subconscious taking over and the significance of it I'm still not completely clear on. Does it usually only take over people who are already pretty hostile and aggressive, does it represent people giving in to their suppressed urges or what? Except the only examples given so far are of already violent and aggressive people getting funny looking eyes and not really drastically changing their behavior in any major way. ('More aggressive' is kind of a vague quantification when already dealing with a conquering army...) Though the example of Alexander's army seems to fit the 'increased hostility' theme more than the whole thing about Genghis Khan.