Flatbusher,
I think the answer that I and others have given explains why Chazal hid sisrei torah in divrei aggada that were not meant to be taken literally. There are 3 types of aggadata:
1. Aggadata meant to be taken entirely literally as a statements of pshat in posuk or historical fact.
2. Aggadata meant to be taken entirely metaphorically to teach hidden aspects of the Torah or to make a rhetorical point.
3. Aggadata that has both a simple literally true meaning and a deaper hidden meaning.
The only issue is how you know what kind of aggadata you are looking at. The first step is to look at the Rishonim (who had a kabalah of how to understand specific sugyas) and see how they interpret the aggada. The second step is to find a Rebbi that can teach you aggadata and how to tell if something is literal or not. You can then learn the various “tells” in an aggadic passage that give away whether it is meant literally or not. For example an aggadata that contradicts mefuresh pesukim is less likely to be literal (e.g. Yakov Avinu lo mes).