How can the temporary update directory be changed?

Impossible. The path is hard coded in many places (wp-admin/includes/update-core.php for example).

I think this is worth a Trac ticket, if there isn’t one already. We can move the directories for plugins, themes and mu-plugins. This is the last thing why we need a wp-content directory at all.

Update

There was a short discussion in ticket #25153. The result is a wontfix, because the upgrade directory enforces the existence of a wp-content directory (whatever its name is in your setup), and that should be kept in case the core needs to add further directories here later, for example wp-content/libraries/.

You can set the upload directory and the wp-content directory to the same physical directory via wp-config.php constants. This should be clean enough for time being.