Here's a readable and technically detailed article about how you build a proper, low-emissions 2.0 liter diesel engine.

The gist seems to be that the TDI's will drop somewhat in horsepower/torque and mileage, but not outrageously so, and aftermarket tuners will be happy to give all of that back to you if you don't care about your emissions.

The deeper thing to ponder is whether VW will have some sort of requirement to "just" repair your car to meet the specs or whether they will need to further compensate you for reducing the vehicle's value and/or give you some outrageously long powertrain warranty to cover any of the issues that apparently come with running a diesel engine "properly".

If I owned one of these cars and VW offered to fix it gratis, give it a long warranty, and cut me a $3000 check, I'd probably say "meh, good enough" and go on with life.