Make the subject box hidden in the reply form.
Change this:
<input type="text" name="Subject" maxlength="{$config['subjectlength']}" class="formboxes" size="60" value="$Subject" /><br />
To:
<input type="hidden" name="Subject" maxlength="{$config['subjectlength']}" class="formboxes" size="60" value="$Subject" /><br />
This way they cannot change it.