Size and From must be applied to the top level query, you are losing them here.
Try this:
$queryString = new QueryString();
$queryString->setFields(array('_all'))
->setDefaultOperator('OR')
->setQuery($terms);
$custScoreQuery = new CustomScore();
$custScoreQuery->setQuery($queryString);
$custScoreQuery->setScript("_score * (doc['section.id'] == 7) ? 0.5 : 1");
$query = new \Elastica\Query();
$query->setQuery($custScoreQuery);
$query->setSize($maxItems);
$query->setFrom(($page - 1) * $maxItems);
$index = $this->get('fos_elastica.index.search_en_gb');
$results = $index->search($query);
Also, turn on the logs in Elastica, and you will be able to see if there is a "size" and "offset" in the Json query. That being said, of course pagination works with custom score.