The Ben Yehoyada (Ben ish chai) (shabbos 22a) explains that the brothers didn't notice that there were snakes and scorpions in the pit, because they were hiding in holes in the walls of the pit. Therefore Reuven had no problem in throwing Yosef into the pit. Even so, the Torah uses the superfluous "the pit was empty, it contained no water" to teach us that there were snakes and scorpions, to teach us Yosef's level, that he was deserving of a miracle to keep him alive.

The Rada"k explains that the brothers did plan on killing him, and knew there were snakes and scorpions. He doesn't mention the contradiction between Reuven's desires and actions.

The Ben Yehoyada (Ben ish chai) (shabbos 22a) explains that the brothers didn't notice that there were snakes and scorpions in the pit, because they were hiding in holes in the walls of the pit. Therefore Reuven had no problem in throwing Yosef into the pit. Even so, the Torah uses the superfluous "the pit was empty, it contained no water" to teach us that there were snakes and scorpions, to teach us Yosef's level, that he was deserving of a miracle to keep him alive. Therefore it's possible to understand this explanation as p'shat, without it contradicting the rest of the passage. (There are other similar versions of this explanation that I've seen in other mefarshim, but this is the general idea)

[The Rada"k explains that the brothers did plan on killing him, and knew there were snakes and scorpions. He doesn't mention the contradiction between Reuven's desires and actions.]