When there's a truck on the tracks, there's not much the people in charge of the train can do about it.
Today's incident appears to be the result of a switch being thrown that diverted the Amtrak train from the main track to the track where the empty freight train was parked. (Although of course no formal finding has yet been made.) The tracks and the switching system in the area where the accident occurred are controlled by the freight company which owns the freight train, not Amtrak.