The Union of Concerned Scientists (UCS), the authors of the sited article, have been debunked several times for using faulty data and questionable conclusions while carrying a left wing political agenda. They are as believable as Consumer's Union in my opinion.
Just another Hate America First organization. Sorry.
Diesel is less refined version of crude oil than gasoline is. Which means, yes, more crude is in a gallon of diesel than a gallon of gas. What you failed to point out is that there is less energy investment in refining that oil to diesel than refining to gasoline. Also diesel can be extracted more easily than gasoline from the dirty crudes. Gasoline is best obtained from the "light sweet crude" (read middle eastern) oils.
However, the core of this article is on emissions. The EPA measures emissions per gallon of fuel used. If a diesel powered vehicle uses 20% less fuel to go 1 mile than a gas powered vehicle, but produces 10% more pollutants per gallon, there is still a net DECREASE in pollutants of 10% in the real (non-government) world.
The EPA laws are mostly governmental spin to stay in bed with the oil companies. They have very little to do with pollution.
Just my observations.