I would write this using a left join rather than as a subquery:

    SELECT pp.page_id FROM page_wikia_props pp LEFT JOIN page p ON pp.page_id=p.page_id WHERE p.page_id IS NULL;

There can be a lot of pages on a wiki which will all be returned by that subquery and there's no chance of an index being used to reduce it.  Also, an explain lists is as 'dependent subquery' which means that MySQL will run that select for every row.