there is a plugin to allow this to happen. and it works quite well actually if you follow instructions.
the main reason wordpress MS does this is to prevent new sites that are created from conflicting with possible categories or tags that are created. for example, having someone create a site called topics while having a category named topics would cause issues. by having /blog slug in the URL for the main site, using subdirectories, this remedies those situations.
however, if you aren't going to allow users to create sites, and you know exactly how your network and categories will be laid out, then you can use said plugin or do it yourself. the only real problem comes from when you have removed the /blog slug and have a site and top level categories/tags that would be duplicated.
if you do allow users to create site with your MS install, then you can simply disallow the categories you have created from being used in the WP admin area, for blog creation.