I see several ways to solve this problem:

1. I agree with Izquierdo you should not design a table inside a pop-up window. But whatever the reason you have to do that please follow the next options.

2. Design it as you described earlier and then test it (the simple one). If users are frustrated consider another interaction. It shouldn't be real code implementation, a simple Figma prototype would be enough. Can be useful here: Framework to Evaluate and Improve the User Experience.

3. Design it as a nonmodal popup. Which appears as a dialog above the popup, but it won't be one more popup on top of the previous one. More about that Nonmodal popups

4. Do not ask for confirmation of deleting, but provide undo option. This decision should be considered with the front-end and backend teams because it solves the UX problem but can cost too much.

The problem is that your modal is outside of your for loop and that you are trying to access the $user variable in your modal. At this point in time the $user variable contains the last element of your for loop, because your loop has already iterated. That is the reason why you are always deleting your last user.

There are 2 options:

1. Put your Modal code into your loop (this will create a modal for each entry)
2. It is good practice to only have one modal and change the values dinamically (like you wanted to do). But for that you will have to pass/build the correct delete URL in your on click method

Give your form an id like id="delete-form" afterwards in your onclick method you can set the action dinamically:

$('#delete-form').attr('action', '/users/' + delete_id);

GET recipe

For this task you can use already available plugins and bootstrap extensions. Or you can make your own confirmation popup with just 3 lines of code. Check it out.

Say we have this links (note data-href instead of href) or buttons that we want to have delete confirmation for:

Copy<a href="#" data-href="delete.php?id=23" data-toggle="modal" data-target="#confirm-delete">Delete record #23</a>

<button class="btn btn-default" data-href="/delete.php?id=54" data-toggle="modal" data-target="#confirm-delete">
    Delete record #54
</button>

Here #confirm-delete points to a modal popup div in your HTML. It should have an "OK" button configured like this:

Copy<div class="modal fade" id="confirm-delete" tabindex="-1" role="dialog" aria-labelledby="myModalLabel" aria-hidden="true">
    <div class="modal-dialog">
        <div class="modal-content">
            <div class="modal-header">
                ...
            </div>
            <div class="modal-body">
                ...
            </div>
            <div class="modal-footer">
                <button type="button" class="btn btn-default" data-dismiss="modal">Cancel</button>
                <a class="btn btn-danger btn-ok">Delete</a>
            </div>
        </div>
    </div>
</div>

Now you only need this little javascript to make a delete action confirmable:

Copy$('#confirm-delete').on('show.bs.modal', function(e) {
    $(this).find('.btn-ok').attr('href', $(e.relatedTarget).data('href'));
});

So on show.bs.modal event delete button href is set to URL with corresponding record id.

Demo: http://plnkr.co/edit/NePR0BQf3VmKtuMmhVR7?p=preview

POST recipe

I realize that in some cases there might be needed to perform POST or DELETE request rather then GET. It it still pretty simple without too much code. Take a look at the demo below with this approach:

Copy// Bind click to OK button within popup
$('#confirm-delete').on('click', '.btn-ok', function(e) {

  var $modalDiv = $(e.delegateTarget);
  var id = $(this).data('recordId');

  $modalDiv.addClass('loading');
  $.post('/api/record/' + id).then(function() {
     $modalDiv.modal('hide').removeClass('loading');
  });
});

// Bind to modal opening to set necessary data properties to be used to make request
$('#confirm-delete').on('show.bs.modal', function(e) {
  var data = $(e.relatedTarget).data();
  $('.title', this).text(data.recordTitle);
  $('.btn-ok', this).data('recordId', data.recordId);
});

Show code snippet

Copy// Bind click to OK button within popup
$('#confirm-delete').on('click', '.btn-ok', function(e) {

  var $modalDiv = $(e.delegateTarget);
  var id = $(this).data('recordId');

  $modalDiv.addClass('loading');
  setTimeout(function() {
    $modalDiv.modal('hide').removeClass('loading');
  }, 1000);

  // In reality would be something like this
  // $modalDiv.addClass('loading');
  // $.post('/api/record/' + id).then(function() {
  //   $modalDiv.modal('hide').removeClass('loading');
  // });
});

// Bind to modal opening to set necessary data properties to be used to make request
$('#confirm-delete').on('show.bs.modal', function(e) {
  var data = $(e.relatedTarget).data();
  $('.title', this).text(data.recordTitle);
  $('.btn-ok', this).data('recordId', data.recordId);
});

Copy.modal.loading .modal-content:before {
  content: 'Loading...';
  text-align: center;
  line-height: 155px;
  font-size: 20px;
  background: rgba(0, 0, 0, .8);
  position: absolute;
  top: 55px;
  bottom: 0;
  left: 0;
  right: 0;
  color: #EEE;
  z-index: 1000;
}

Copy<script data-require="jquery@*" data-semver="2.0.3" src="//code.jquery.com/jquery-2.0.3.min.js"></script>
<script data-require="bootstrap@*" data-semver="3.1.1" src="//netdna.bootstrapcdn.com/bootstrap/3.1.1/js/bootstrap.min.js"></script>
<link data-require="bootstrap-css@3.1.1" data-semver="3.1.1" rel="stylesheet" href="//netdna.bootstrapcdn.com/bootstrap/3.1.1/css/bootstrap.min.css" />

<div class="modal fade" id="confirm-delete" tabindex="-1" role="dialog" aria-labelledby="myModalLabel" aria-hidden="true">
  <div class="modal-dialog">
    <div class="modal-content">
      <div class="modal-header">
        <button type="button" class="close" data-dismiss="modal" aria-hidden="true">×</button>
        <h4 class="modal-title" id="myModalLabel">Confirm Delete</h4>
      </div>
      <div class="modal-body">
        <p>You are about to delete <b><i class="title"></i></b> record, this procedure is irreversible.</p>
        <p>Do you want to proceed?</p>
      </div>
      <div class="modal-footer">
        <button type="button" class="btn btn-default" data-dismiss="modal">Cancel</button>
        <button type="button" class="btn btn-danger btn-ok">Delete</button>
      </div>
    </div>
  </div>
</div>
<a href="#" data-record-id="23" data-record-title="The first one" data-toggle="modal" data-target="#confirm-delete">
        Delete "The first one", #23
    </a>
<br />
<button class="btn btn-default" data-record-id="54" data-record-title="Something cool" data-toggle="modal" data-target="#confirm-delete">
  Delete "Something cool", #54
</button>

Demo: http://plnkr.co/edit/V4GUuSueuuxiGr4L9LmG?p=preview

Bootstrap 2.3

Here is an original version of the code I made when I was answering this question for Bootstrap 2.3 modal.

Copy$('#modal').on('show', function() {
    var id = $(this).data('id'),
        removeBtn = $(this).find('.danger');
    removeBtn.attr('href', removeBtn.attr('href').replace(/(&|\?)ref=\d*/, '$1ref=' + id));
});

Demo: http://jsfiddle.net/MjmVr/1595/

Apps handle this situation all the time, and you're correct pop-up/modal confirmations are not usually a good option.

Here's an example: A sales representative opens up a modal in order to delete a contact, a vendor, or whatever. On selecting submit a div is revealed asking "Are You Sure?" When the rep presses yes the delete goes through.

If the representative still has more actions to complete on the modal then the modal remains open. Depending upon your app there may be no need for the modal to remain open in which case the modal can close as well. Bear in mind, depending upon your users, and how this fits into their work expectations, the double action (form submission and closing the modal) may be very unsettling so it may make sense to tell the user that on submission the modal will close and he will be returned to original page.