By polluting... The various emissions from a diesel engine (the gases other than CO2) are all toxic, and cumulatively affect the health of those who breathe those emissions (ie. people in cities).
More directly, VW's excess polluting caused people to die. How many is hard to say for sure but almost certainly more than any of the recent safety related automotive engineering design screwups lately such as Toyota's "unintended acceleration" problem and GM's bad switches.