In the comics, it wasn't Flint Marko who was responsible for Uncle Ben's death. The storylines usually have different characters or events leading to this tragic event.
A fanfic could start with Ben being sent to the Kill la Kill universe through some sort of interdimensional rift. In this new world, he discovers that the Omnitrix can absorb the power of Life Fibers. This leads to a race between the heroes and the villains of Kill la Kill to either use Ben's newfound ability for good or to take it over for evil. Ben has to learn the ways of this new world quickly while also trying to find a way back home.
Well, Jacob deceived Esau in two main ways. Firstly, he exploited Esau's hunger. Esau was so hungry that he was willing to trade his birthright, which was a very important thing in their culture, for a simple bowl of stew. Then, to get the blessing, Jacob followed his mother's plan. He disguised himself as Esau. He wore Esau's clothes, which would have had Esau's scent on them, something that their blind father Isaac could recognize. And he used goatskins to make his skin feel hairy like Esau's. This way, he managed to deceive Isaac into giving him the blessing that was rightfully Esau's.
Satsuki Kiryuin and Ben would be really interesting. Satsuki is so calculating and in control. When she meets Ben, she would probably be intrigued by his Omnitrix and see it as a potential tool for her own plans. Ben, on the other hand, would be wary of her motives. Their interactions would be full of power plays and mind games as Ben tries to figure out if Satsuki is an ally or an enemy while Satsuki tries to manipulate Ben into doing what she wants.
In the Qing Yu Nian novel, Barrette shot and killed the Qing Emperor's two brothers, helping the Qing Emperor ascend to the throne. Fan Xian had used a sniper rifle to kill Yan Xiaoyi. In the battle with the Qing Emperor, he had also inflicted serious injuries on the Qing Emperor. Fan Ruoruo had also used a Barrett sniper rifle, but the specific information on who she killed was not in the search results provided.