Update:
See the comment about adding "@Table(name="table_name",options={"engine"="MyISAM"})" , it is the better answer.
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This is untested code aimed to help you get to an answer, you will need to read a lot of Doctrine2 code to figure out what you want though. I spent about 30mins reading code and couldnt find a way to push the $options array through the ORM layer to this DBAL layer function.
check out Doctrine/DBAL/Platforms/MySQLPlatform.php
427 // get the type of the table
428 if (isset($options['engine'])) {
429 $optionStrings[] = 'ENGINE = ' . $options['engine'];
430 } else {
431 // default to innodb
432 $optionStrings[] = 'ENGINE = InnoDB';
433 }
try hard coding what engine want in there. It will almost certainly break stuff though (eg, foreign keys dont work in MyISAM)