If you want to do this only in PHP, you will need to add "steps" in your script, like:
step1 (show form) -> step2 (ask validation) -> step3 (validate)
To do so, you can use sessions to keep form content, and GET parameter to track the step. Otherwise the simplest solution is to use javascript:
echo "<td><a onClick="javascript: return confirm('Please confirm deletion');" href='delete.php?id=".$query2['id']."'>x</a></td><tr>"; //use double quotes for js inside php!