Navalny does have a lot of enemies: if you look at this page https://fbk.info/investigations/ (use Google translate), you will see mentions of dozens of people. He keeps investigating into them in great detail and exposing their illegal wealth. They aren't that nameless, they are rich and powerful people, some of them are sure to have friends within GRU.

Not saying that Putin didn't order it, just pointing out that the group of people with motive and means to do it is bigger than just him.