Count Pitchers' Batting Stats
If your player produces stats that your league selected for scoring, they should count. Your player's hitting stats shouldn't be omitted just because he pitches. You can make it an option to erase pitchers' hitting stats if people don't like that concept, but the default shouldn't be to erase stats arbitrarily.
I make this argument every year in some fashion, doing the same now. Yahoo wrote back to me many years ago on this, saying essentially that pitchers' batting stats aren't counted because they're not good. Unsatisfactory explanation, but since it's the only one Yahoo's provided, my response is where do you draw the line between good and bad. There are no rules saying that certain position players' stats are omitted if they're not "good" enough. Yahoo hasn't written back to me since.