The occupants of the trolley had intentionally run over many people in the past. Ender had reason to believe that they intended to do so again. We only have th

The occupants of the trolley had intentionally run over many people in the past. Ender had reason to believe that they intended to do so again. We only have the word of the dormant hive queen that they didn't intend to again. (Spoiler Alert) In the Shadow series, it's revealed that the hive queen lied to Ender about some things. The formic males struck a deal with Bean's children to keep Ender from finding out. Even if he had known, his actions were still just.