My roommate is half Greek and she learned this tradition from her mother. She explained that the spitting is to prevent the compliment from going to their head and inflating their ego.
This is interesting because it promotes a humitity above all else. This custom illuminates a light on a culture which retains a mentality that people are ordinary and must always remember that. This seems to be particularly strong in Greek culture where they had a theological system where gods were very similar to humans, they experiences human desires and intereacted with humans on a regular basis. As a result people were very aware that they were less than gods, who weren't that special to begin with, leading to a humility and a custom that exists to prevent egos from being inflated.