Article One is not an Everything Proof Shield, it is a vague platitude about values. We say no thanks the emperor says 'As the Heir of Magnus and Sigmar's Holy Empire I command you do do it.' What do we do then, just insult him and blithely assume there will be no fallout from him or his faction?
This really feels like fearmongering. What would we do if we were Loremaster at large and the Emperor ordered us to assassinate a Dwarf King, or even Belegar? What would we do if we were researching Waystones and the Emperor ordered us to stop?