You are already selecting from the mdl_user table so just add the username column, like this (roughly and untested!):
SELECT
d.DATE,
d.COUNT,
'(' + d.username + ')'
FROM
(
SELECT
u.timecreated,
DATE_FORMAT(FROM_UNIXTIME(u.timecreated), '%M %Y') AS DATE,
u.username,
(CASE WHEN (u.deleted = 0) THEN 1 ELSE 0 END) AS COUNT
FROM
mdl_user AS u
GROUP BY
YEAR(FROM_UNIXTIME(u.timecreated)) MONTH(FROM_UNIXTIME(u.timecreated)), u.username, u.deleted
) AS d