I found
this article, entitled "Behind the Wall: East German football between state and society." (in English) It's rather interesting material, touching on the links between the SED (Socialist Unity Party/the government) and the football clubs, as well as links between West German fans and their Ossi counterparts (most notably in Berlin itself, where Hertha fans would meet Union fans in East Berlin). It's a bit long, but worth the read. It makes a nice companion to Uli Hesse's Tor! (I assume; I'm broke & haven't bought it yet.)
And regarding Hertha and Union fans, and today's travesty of a match, European Football Weekends discusses the
derby with no history. (English)
Regarding former-GDR clubs in reunified Germany, DW-World (English) ran
this story back in September about the difficulties Ossi teams have competing with Wessi teams.