It occurs to me another way to optically isolate the Arduino from the PC would be to use a bluetooth or wifi radio device.
One way to use fiber is to use it as a network device. Recently, I was curious and did a google search, and saw you could get low end ethernet->fiber converters for about $50 each. Couple that with an ethernet shield should get you the connection.
The post BlinkIt in the exhibition gallery shows another way to communicate: http://arduino.cc/forum/index.php/topic,140698.msg1057787.html
, and presumably you could use it via a fiber optic cable if you could put a light sensor on the PC.