You can use the filter filter ;) using a function instead of a string in the expression argument. Remember this is the syntax of filter
{{ filter_expression | filter : expression : comparator}}
The expression can be a string, an object or a function. Something like this will do
$scope.filterUnemployed = function(value) {
    var jobs = $scope.job.data;
    for (var i = 0; i < jobs.length; i++) {
        // Search every object in the job.data array for a match. 
        // If found return false to remove this object from the results
        if (jobs[i].user.name === value.name) {
            return false;
        }
    }
    // Otherwise return true to include it
    return true;
}
And then apply the filter to your ng-repeat directive like this
<ul ng-repeat="a in user.data | filter:filterUnemployed">
    <li>
        <md-checkbox>
            {{ a.name }}
        </md-checkbox>
    </li>
</ul>
Note that this will not modify your original collection but will result in a new copy beign displayed in your html since this is usually the desired effect.
Check the sample for a working demo
angular.module('app', [])
  .controller('SampleCtrl', function($scope) {
    $scope.user = {
      data: [{
        name: 'John'
      }, {
        name: 'Mary'
      }, {
        name: 'Peter'
      }, {
        name: 'Jack'
      }, {
        name: 'Richard'
      }, {
        name: 'Elizabeth'
      }]
    };
    $scope.job = {
      data: [{
        jobTitle: 'CEO',
        user: {
          name: 'John'
        }
      }, {
        jobTitle: 'CFO',
        user: {
          name: 'Mary'
        }
      }, {
        jobTitle: 'Analist',
        user: {
          name: 'Jack'
        }
      }]
    };
    $scope.filterUnemployed = function(value) {
      var jobs = $scope.job.data;
      for (var i = 0; i < jobs.length; i++) {
        if (jobs[i].user.name === value.name) {
          return false;
        }
      }
      return true;
    }
  });
<script src="https://ajax.googleapis.com/ajax/libs/angularjs/1.2.23/angular.min.js"></script>
<div ng-app="app" ng-controller="SampleCtrl">
  <h1>All Users</h1>
  <ul ng-repeat="a in user.data">
    <li>
      <md-checkbox>
        {{ a.name }}
      </md-checkbox>
    </li>
  </ul>
  <h1>Unemployed users</h1>
  <ul ng-repeat="a in user.data | filter:filterUnemployed">
    <li>
      <md-checkbox>
        {{ a.name }}
      </md-checkbox>
    </li>
  </ul>
  <h1>Employed</h1>
  <ul ng-repeat="x in job.data">
    <li>
      <md-checkbox>
        {{ x.user.name }}
      </md-checkbox>
    </li>
  </ul>
</div>