These work
SET GLOBAL LOG_SLOW_TIME = 1;
SET GLOBAL LOG_QUERIES_NOT_USING_INDEXES = ON;
Broken on my setup 5.1.42
SET GLOBAL LOG_SLOW_QUERIES = ON;
SET GLOBAL SLOW_QUERY_LOG = ON;
set @@global.log_slow_queries=1;
http://bugs.mysql.com/bug.php?id=32565
Looks like the best way to do this is set log_slow_time very high thus "turning off" the slow query log. Lower log_slow_time to enable it. Use the same trick (set to OFF) for log_queries_not_using_indexes.