Se você estiver usando o MySQL 5.5, tente usar uma inserção atrasada em vez de inserir.
When you use KILL, a thread-specific kill flag is set for the thread. In most cases, it might take some time for the thread to die because the kill flag is checked only at specific intervals: [...]
An INSERT DELAYED thread quickly flushes (inserts) all rows it has in memory and then terminates.
The queued rows are held only in memory until they are inserted into the table. This means that if you terminate mysqld forcibly (for example, with kill -9) or if mysqld dies unexpectedly, any queued rows that have not been written to disk are lost.