Brian Wheeler has had an interview with MMORPG.com and he says that you will need to have the vampire and werewolf skill lines to counter them in pvp. http://www.mmorpg.com//gamelist.cfm/setview/features/loadFeature/8237/gameID/821/utm_campaign/MMORPG%20Daily%20Digest%20Email/utm_source/MMORPG/utm_medium/email/eatrack/fenlander@btopenworld.com,8
So I guess the Fighters Guild skill line touted as the natural counter is not that powerful then.
Quoted in case you don't wish to read it all.