A few quick questions (apologies if you’ve already tried these…):
1.) Does the following not work?
Go to Network Admin -> Sites -> Edit Site (for the main site)
Find the permalink structure and remove /blog/
My searching suggests that, so long as you edit that, and not the permalink under the site config (which will then re-insert a mandatory “/blog” slug), it might work…
2.) Assuming you had already tried that (and the existence of the plugin I’m about to mention suggests that the above can’t be the answer):
Have you tried the “remove /blog slug plugin for wpmu?
3.) The .htaccess solution would be problematic, I suspect, because WordPress won’t know which site to serve without a corresponding database entry…