HTML:

<ya-map ya-zoom="8" ya-center="[37.64,55.76]" ya-after-init="afterMapInit($target)"></ya-map>
<button ng-click="del()">Удалить</button>
    

javascript:

var _map;
$scope.afterMapInit = function(map){
    _map = map;
};
$scope.del = function(){
    _map.destroy();
};