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I've been running like this for a few days and it seems that I was hasty in making the recommendation. Disabling autocommit automatically makes mysql start a transaction (meaning that calling BEGIN is now optional), which can make for some very long transactions if you have a persistent connection that only issues select queries. Additionally, those transactions will be stuck in an isolation level that prevents them from seeing any changes to the database that were issued after the transaction was created.
You can of course set the isolation level to "read committed", but that behavior may surprise people who are used to the default isolation level. More info is here if you want some docs on isolation levels:
http://