borax is the mold killer, it goes right to the root and kills it dead. you can make a kind of thick sludge with it and work it into the carpet with a brush. its more affective than bleach and there are no fumes. once it dried you can lift hte carpet and just sprinkle some underneath, replace the carpet and just leave it there for a few days to make sure its fine.
you can also put a dehumidifier in your car overnight. make sure its completely sealed off, this will dry out the car. mold need moisture to live.
tea tree oil is also good, but it has a powerful scent.
hydrogen peroxide will also work, but it doesn't stay active for very long once you pour it into the carpet.