I would go for the VW TDi, and here's why.
First, as you say, diesel does get better mileage on the highway than hybrids. Hybrids get great mileage in city driving, but on the highway they get about the same as the city or sometimes less, because the gas engine is running more.
The TDi should get 50 - 60 mpg on the highway. Also, diesels will last 200,000+ miles easily.
As for the fuel cost, diesel does cost more than gas right now. I don't know if that will change or not. You'd think that diesel would be cheaper, but that isn't the case. However, you could make your own biodiesel, and save lots of money. You can buy a biodiesel kit for about $2,000 and use it to make up 40 gallon batches of bio diesel for a total cost of about $0.70 to $1 per gallon, assuming you can get used cooking oil for free. (You should be able to make some deals with some local restaurants to pick up their cooking oil for free.) The TDi will run on this biodiesel fine, with no modifications to the car.
You do have one other option: you can check out a regular, non-diesel or non-hybrid car, which would be cheap to purchase, that gets mid-30s or better on the highway. Calculate how many miles you will commute, how much fuel you will use, and compare the cost using the price of gasoline vs. the price of diesel... and compare that to the money saved by buying a used, gasoline-powered car. I had a 1997 Honda Civic HX 5-speed that was rated at 37 mpg city, 45 mpg highway, and I was able to get the rated 45 mpg on the highway. Obviously that's an 11-year-old car now, so finding one in good condition might be hard, but might be worth a look.
I think if I had a long commute though, and was buying a newer car, I would go the TDi route and make my own biodiesel.
A Porsche will get you through periods of no women better than a woman will get you through periods of no Porsches. - somebody really wise.