After a little digging through the source I found there is a filter called woocommerce_single_product_carousel_options
that can be used to modify the flex slider options
for example:
function my_product_carousel_options($options) {
$options['animation'] = 'fade';
return $options;
}
add_filter("woocommerce_single_product_carousel_options", "my_product_carousel_options", 10);