“at least in the times of the geonim and the rishonim”
Or today. Rabbi Avraham ben HaRambam’s essay on how to understand aggadata is used as the introduction to the Ein Yaakov collection of aggadata.
Furthermore it should be noted that the classical commentaries often bring down interpretations that stray far from the pshat of the text. (I’ve already mentioned the example of the flood not covering the entire world.) While pshat is very important, we are not permitted to dismiss these commentaries chas v’shalom! Judaism has never been exclusively literalist in its biblical interpretation.