Relevant:
http://core.trac.wordpress.org/ticket/12002
/blog/ is added to prevent permalink clashes on the root site of a multisite install. For now you’re going to have to resort to using the network admin and manually wading through the options table modifying it each time you regenerate rewrite rules.
You can remove the blog slug completely.
Go into the primary site options in the network admin, and set your permalinks without blog included, to something like /%postname%/. Go back to the permalinks settings in your site’s dashboard, you should notice that /blog is removed from the permalinks. Set them to your desired structure again and save.
This should remove the blog slug from your URLs.