A quick example of using theme_field to change the price field right before being rendered.

template.php

<?php
/**
 * Implements theme_field()
 */
function THEMENAME_field__commerce_price($variables) {
  if ($variables['items'][0]['#markup'] == '$0.00') {
    return '<div class="commerce-product-field field-commerce-price sr-only">Call for pricing.</div>';
  } else {
    return;
  }
}