Well, the way Peter killed MJ in the comics could vary depending on the storyline and the creative direction of the writers. Sometimes, it could be due to complex plot developments or conflicts within the comic universe.
Peter could be a disgruntled noble in the fanfiction. He might be someone who has been overlooked for promotions or honors by the emperor, and this has led to his resentment and desire to kill the emperor.
One possible motive could be political ambition. Maybe Peter wants to take over the emperor's power and position in the fictional world. If the emperor has a lot of control and influence, Peter might see killing him as a way to gain that for himself.
In the fanfiction, Peter Quill Parker might have some new powers or gadgets that give him the edge. He could have studied Thanos' fighting patterns and found a way to counter them. Also, his quick thinking and ability to improvise in tough situations would play a big role. He might even use his charm to get close to Thanos and then strike when he least expects it.