First, you're flat-out wrong.  The Church has NEVER held that conscience is the determinant of the moral content of an action nor that conscience can turn an objectively evil act into something objectively good.  Good heavens, man.  
Second, yes, the Church acknowledges the critical role of conscience but has always qualified the concept by placing it within the framework of a conscience correctly formed and informed. 
Third, if one were to assign primacy to conscience, then there is literally no action, however monstrous or evil, that could not end up being somehow rationalized.  This is contrary to logic, reason, and, yes, Church teaching.  
Finally, I'll repeat the question I posed elsewhere in this thread: if a Nazi guard at Auschwitz participates in mass murder, can he later, as a matter of moral reasoning, justify the crime as a product of his (convoluted) "conscience"?  
I won't hold my breath waiting for an answer.