todoFactor and TodoCtrl modules for the angularFire TodoMVC example to show an alternative example for using angularFireCollection to sync data with a Firebase by using a Factory to do so. https://github.com/firebase/angularFire/issues/24

todoCtrl.js

'use strict';
todomvc.controller('TodoCtrl', [ '$scope', 'todoFactory', 'filterFilter',
	function OtherCtrl($scope, todoFactory, filterFilter) {
		$scope.todos = todoFactory.getAllTodos('todos');
		$scope.newTodo = '';
		$scope.editedTodo = '';
		$scope.addTodo = function() {
			todoFactory.addTodo($scope.newTodo);
		};
		$scope.editTodo = function(todo) {
			$scope.editedTodo = todo;
			todoFactory.editTodo(todo);
		};
		$scope.doneEditing = function(todo) {
			$scope.editedTodo = null;
			if (!todo.title) {
				$scope.removeTodo(todo);
			}
		};
		$scope.removeTodo = function(todo) {
			todoFactory.removeTodo(todo);
		};
		$scope.markAll = function(completed) {
			$scope.todos.forEach(function (todo) {
				todo.completed = completed;
			});
		};
	}
]);

todoFactory.js

'use strict';
todomvc.factory('todoFactory', [ 'angularFireCollection',
	function todoFactory(angularFireCollection) {
		var url = 'https://angularFire.firebaseio-demo.com/todomvc';

		return {
			addTodo: function(newTodo) {
				this.getAllTodos('todos').add({
					title: newTodo,
					completed: false
				}, function() {

				});
			},
			getAllTodos: function(path) {
				var ref = angularFireCollection(url + '/' + path);
				return ref;
			},
			editTodo: function(todo) {
				this.getAllTodos('todos').update(todo);
			},
			removeTodo: function(todo) {
				this.getAllTodos('todos').remove(todo);
			}
		};
	}
]);

In this example, what exactly are you passing to the .remove(todo) method call in your todoFactory.js file? I am using your gist as a guide in my own application and am having trouble with the remove method. What does the remove method accept as an argument to uniquely identify the todo that you are trying to delete?