Fluff: Question Sisters of Sigmar vs Witchhunters.

My Question is: What kind of relation has the Sisters of Sigmar and the Witchhunters has?

According to the official rulebook, most politically minded Sigmarites of the Empire consider the Sisters to be unworthy. while the witch hunters consider them to be heretics. The Sisters possess an item called The Script of Sigmar in their convent, The Rock, and the witch hunters desperately wish to claim it. The Sisters were exterminating any survivors of the comet blast believing themselves to be the only Sigmar worthy survivors. I’m assuming your question has to do with possible alliances so between Sisters and Old Lady Burners I would say no, but then again anything can happen with the right story line.

In that case is it more likely to Sisters never form an alliance if we go with "strick fluff" ?

I don't like to use the word 'never' when dealing with background or 'fluff'. Let's just say it would be highly unlikely for Sisters and Witch hunters to form an alliance under normal circumstances as indicated in the rule book. You and your group should decide if there may be unusual story/campaign circumstances that would say otherwise. Think of it as House Fluff. As a universal example look at the Terminator movies. Terminators were created for the annihilation of mankind yet most of the movies dealt with a Terminator helping save mankind. Fluff is just fluff, it should be fun not strict. Hope that helps.