One way to return a HAL entity from an Apigility RPC controller.

rpc-hal-entity.php

<?php
public function someAction()
{
    $data = doSomeWorkFetchSomeData();
    $entity = new \ZF\Hal\Entity($data, $data['id']); // or similar
    return new \ZF\ContentNegotiation\ViewModel([
        'payload' => $entity,
    ]);
}

Incase someone else has this problem.
You can use the Hal plugin that the Rest controllers use to generate Hal entities containing links:

<?php
    public function anRpcAction()
    {
        $entity = $this->getEntityFromSomewhere();

        $route = $this->getEvent()->getRouteMatch();

        return new ViewModel([
            'payload' => $this->Hal()->createEntity($entity, $route, $route->getMatchedRouteName())
        ]);
    }

If you havn't defined a REST service for the entity you want to return, you might need to configure the metadata map by hand

'zf-hal' => [
        'metadata_map' => [
            'User' => [
                'route_name' => 'api.rest.user',
                'entity_identifier_name' => 'username',
                'route_identifier_name' => 'user_id',
                'hydrator' => 'Zend\Stdlib\Hydrator\ObjectProperty',
            ],
        ],
    ],