How to calculate the percent of mitochondrial heteroplasmy
I emailed the authors of the paper "Age-Related Accumulation of Somatic Mitochondrial DNA Mutations in Adult-Derived Human iPSCs" and they confirmed that they calculated the % of mtDNA heteroplasmy by the following: 
Aligned all mtDNA genomes against the reference sequence. Any deviance at a specific position from the reference was a "mutation". The % heteroplasmy was calculated by dividing the total number of mutations at a certain nucleotide position by the total number of genomes represented at the position multiplied 100. 
So in other words, to go back to my original question- if there were 10,000 genomes aligned and there were 700 mutations at the same position, that mutation would have 7% heteroplasmy.