object-transform.js

DS.Adapter.registerTransform('object', {
  serialize: function(obj) { return obj; },
  deserialize: function(obj) { return obj; }
});

MyApp.MyModel = DS.Model.extend({
  location: DS.attr('object')
});

var model = MyApp.Model.createRecord({ location: { lat: 123, lng: 456 } });

model.save();

model.set('location.lat', 789);

model.get('isDirty'); // false

// Normally this happens automatically, but in this case you're setting the contents of an object so Ember Data doesn't see the
model.attributeWillChange(model, 'location');

model.set('location.lat', 789);

// Paired with above
model.attributeDidChange(model, 'location');

model.get('isDirty'); // true

It's actually worth seeing if, instead of calling attributeWillChange and attributeDidChange, if just resetting location to itself works, i.e. model.set('location', model.get('location')). I'm not sure that this alternative will work though since Ember Data might not think it was an actual change since the object is the same.