The driver clearly had a Green light, and the emergency vehicle clearly didn't make sure the intersection was clear and everyone was yielding before preceding.
That said, the driver seems like a dummy. I saw the unedited dash footage a few days ago, and the emergency lights are clearly visible on the van from a long distance away... and as pointed out, all the other drivers were slowing at stopping at the intersection. That alone should have been a clue that something was amiss. What if the other drivers were slowing and stopping because a kid was running out into the crosswalk? When other drivers react weird, you always need to make sure you double check your surroundings and assumptions.
Furthermore, when the agents approach the driver at the scene of the accident they aren't claiming he ran a red light, they were saying "didn't you see the red light?!" which I interpret to mean their flashing emergency red lights.
Granted, I haven't read the police report, but from the video and statements the driver has put together, it's clear that he's 1) not a defensive driver and 2) still not clear about what happened (since he's convinced the agents were saying something they weren't). Of course it's also clear that the agents didn't effectively clear that intersection before proceeding through it.
Blame all around.
$0.02