Agree, the karma below -4 counting, but not being shown would be an issue to calculate the average karma per user — but turns out that it appears submissions only add karma to users total karma, so assuming that it is true submission upvote karma is worth 0.5 regardless of context, then to get the average karma per submission simply sum the karma of all submissions, multiple by 0.5, then divide by count of submissions including the flagged and/or killed submissions; to see those, go to your profile, select show dead. To get the average karma per comment, just take the sum of the submission karma above, multiply it by 0.5, then take that amount and divide it by the count of comments by user including the flagged comments.

If I have missed something, let me know.