My take on the horse scene is that the horse, being an animal should abandon the ship as not to follow the rest of the maniacs to... hell. Yes, hell.
The film is highly symbolic and allegorical and I feel that the whole concept is based on a trip without return to hell. Aguirre's sick megalomania and vanity leads the also greedy crew to follow him to a symbolic hell, that Herzog portrays through jungle fever and ultimate death. The horse goes ape before the final stage of the trip, when they go full downhill and insane, and is therefore left behind in this beautiful surrealist scene.
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