I found a work around by setting drop
= TRUE and then changing the stat_summary_hex
function to return NA when the result was less than my threshold:
stat_summary_hex(aes(x = Lon, y = Lat, z = Churn),
bins=100, colour = NA, geom = "hex", drop = TRUE,
fun = function(x) if(abs(sum(x)) > 5) {sum(x)} else {NA})