Dissimilarity Matrix of non-metric proximity data
Maybe I did not completely understand your question, but I think the answer you are looking for is one of the following:


You may want to fill a n-by-n matrix with 1 if the person $i$ has sent e-mail(s) to person $j$, 0 otherwise
Maybe you want to fill the n-by-n matrix with the number of emails sent from person $i$ to person $j$.


Both measures are distances in the mathematical definition.

For clarity:

You could program the dissimilarity matrix as $M[i,j] = 1$ if the pair of people in your data exists.