From what we can tell from watching Trek, the Klingon Empire is an Empire of subjugated planets and civilisations. This means the Klingons are a dictatorship and have conquered planets and took away freedoms and democracy. To change this would result in the collapse of the Klingon Empire. So how can the Federation morally and ethically and in all good conscience become an ally and officially sign an alliance agreement with such an entity as the Klingon Empire? The Klingon Empire goes against everything the Federation stands for.