I do not believe that you will be able to get a 'pop-up' box to be displayed within the trigger. However, what you could do is to override the button that you are using a javascript function that would create a 'pop-up' for the user to 'confirm' their action if they do confirm it to then proceed with the logic of the page, if they cancel their action then to cancel.
If you have jQuery loaded you could do something like the following:
<script type="text/javascript">
jQuery.noConflict();
jQuery(document).ready(function() {
jQuery('.Action').click(function(e) {
if ( confirm('Are you sure you want to delete this record? Click OK to delete.') ) {
return true;
}
e.preventDefault();
});
});
</script>
<!-- somewhere on your page is your button -->
<apex:commandButton action="{!save}" value="Save" styleClass="Action" />
Another option you could do is render a checkbox if the value of the record is one that would require confirmation. This could be done on the selection of the value of the object, or could be done by creating an addError and the page looking for a specific error value before displaying the additional checkbox on the visual page. Then make sure that it is checked prior to doing your actual delete.
