I understand that you think you have a good theory, but the fact that Flood dont utilise technology when the Precursors were tier 0 is a problem. Also, the "mantle" is the main objectionary point against your idea.

 The forerunner tried to contain the flood to study it, because they knew the flood would return eventually, and hopefully by then they would know how to counter it.

And Gravemind's quote is referring to cortana because he also says "you will show me what she hides!" She was hiding the index from gravemind.