Note that this question applies to Ember Data pre-1.0 beta, the mechanism for loading relationships via URL has changed significantly post-1.0 beta!
Instead of an array of ids, the payload needs to contain "something else" than an array.
In the case of the RESTAdapter, the returned JSON is like that:
{blog: {id: 1, comments: [1, 2, 3]}
If you want to handle manually/differently the association, you can return a JSON like that instead:
{blog: {id: 1, comments: "/posts/1/comments"}
It's up to your adapter then to fetch the data from the specified URL.
See the associated test: https://github.com/emberjs/data/blob/master/packages/ember-data/tests/integration/has_many_test.js#L112