The Girls und Panzer announcement also didn’t specify anything about doujin manga.
However, it looks like Girls und Panzer is looking to restrict doujinshi for the series, along with other unofficial merchandise.
They announced the restriction via twitter where the staff said that they will consider the production and sales of any unofficial Girls und Panzer merchandise as copyright infringement.
These include bootleg merchandise or unofficial copies of actual Girls und Panzer merch.