If it helps any, the whole thing started in Fantastic Four #533–535 and culminated in New Avengers Illuminati #1. Another example of Bendis ignoring what was written and making his own continuity.
https://www.cbr.com/hulk-las-vegas-illuminati/
In my mind, I chalk it up to Secret Invasion happening at the time, and SHIELD was heavily infiltrated. There was a backup (or one shot) I believe.. maybe it was online, but it was basically Skrull intelligence files evaluating heroes and how easy/difficulty it would be to swap them out/masquerade as them. The Hulk was listed as very dangerous and that they shouldn't get involved with him, suggesting he should be re-routed or tied up so he can't interfere. So to me, that SHIELD agent (read: Skrull) lied to get the Hulk exiled/killed by the heroes.