Heteroplasmy Calculation
Heteroplasmy at any site (as long as it's a reliable variant) suggests that there is mitochondrial heteroplasmy, it doesn't matter where it is. In that case, the "mitochondrial heteroplasmy" statistic would simply be the maximum value at any [reliable] location.

Due to the low amount of variation in the mitochondrial genome, and because it's a haploid genome, I don't think that a calculation like "average heteroplasmy" makes much sense for mitochondria.