The answer is to change the order of the echo:
<section class="thumb_item">
<?php if (get_post_meta($post->ID, 'price', true) !== '') { ?>
<span class="price"><?php
// Moved the following line from the end to here so echos price first
echo get_post_meta($post->ID, 'price', true);
// Now echo the currency symbol
if(get_option('currency') != ''){
echo get_option('currency');
}else{
echo get_option('currency_symbol');
}
?></span>
<?php } ?>