I am sure someone can quote chapter and verse of the NCAA regulations, but as far as I know, the only exception ... where a player might not lose the year of eligibility ... would be if he incurred a season ending injury, and then there are still restrictions on that as to number of appearances/games played as a percentage of total games for the season.
Basically, as far as I know, if a player pinch runs one time for another player during the season, he is considered to have used a year of eligibility. It's tough but then it IS the NCAA ... !!!