You have to edi6t the my.ini/cnf and put following under the section mysqld
binlog_format = ROW
If you add it under another section it will not work.
You have the right idea to flush first the logs and the switch at runtime to another format, and having the my.cnf changed.
FLUSH TABLES WITH READ LOCK;
SET GLOBAL binlog_format = 'ROW';
What "import" mechanism was used? Some will automatically postpone the secondary-index creation for you.
I don't understand "I'm using stored procedure and with indexes it was very very slow". SPs being used for the import? Or indexes interfering with SPs? What?
Is /tmp on the same disk and in the same disk 'partition'? This is critical ...