I blocked a directory in my site that is not secret but meant for internal discussions that are not relevant for search engine results. After running "Search as Google" at Google Webmaster Tools, the result was a 301 - Moved Permanently. Is this supposed to happen or can this be a black hat cause for my website?
There are many ways to restrict access to content on your site. A lot of Content Management Systems issue a permanent redirect to a generic "You are not allowed" page or the homepage in that case.
Let's say your software verifies that you previously logged in at example.com/login/ when you try to access example.com/index.php?id=123. If you did not, it redirects you to example.com/login. Some tools let you stay on the page (...index.php?id=123) but display a login screen for authentication, verify the credentials you submit and then display the content.
But this is all just convenient for the users. The software could also block with a HTTP response code (like 403) with or without a human readable description about the cause.
What you probably want as you say it's a directory: Create an entry in your robots.txt to disallow bots access to it. This way they know they should not index the page or content below that directory (it's not for the general public anyway).