Delete from data cache operation is slow

The delete SQL command is quite slow on my system. Running this query directly on the DB is also very slow. It doesn’t appear to be missing any indexes. Any ideas?

DELETE FROM wp_popularpostsdatacache WHERE id IN (
SELECT c.id
FROM (
SELECT id
FROM wp_popularpostsdatacache
GROUP BY id
)c
LEFT JOIN wp_posts p ON c.id = p.ID
WHERE p.ID IS NULL
OR p.post_status =  'trash'
)

This query is also always showing up in my New Relic “Most time consuming” log:

INSERT INTO wp_popularpostsdatacache (id, day, day_no_time) VALUES (?, ?, ?) ON DUPLICATE KEY UPDATE pageviews = pageviews + ?, day = ?, day_no_time = ?;

http://wordpress.org/plugins/wordpress-popular-posts/