__() is deprecated in magento. You may either manually delete it from the magento core files (& repeat this process again everytime you have a new install or you upgrade) or wait for magento developers to remove this.
For wordpress, in the future when php 5.3 is much more common & wordpress breaks their backward compatibility & push all their code to namespaces then only this will be solved. I think this won't be anytime soon(maybe never?).
BOTTOM LINE: Since wordpress relies on this function for some functionality & it's deprecated in magento, go for deleting it from core files in magento. You already have the path & line number (\app\code\core\Mage\Core\functions.php:93)
If this doesn't work for you, you can't do what you asked for in the question. My suggestion for an alternative is to create a wordpress script which could dump the required information to some database then create a magento script to read it from there & run them individually (maybe setup a cron)