Mutation is the norm and being normal is not. But what does that mean in a social context? Do the mutants represent a massive, suppressed underclass that is hated and feared by the relative minority of the Imperium's normal population, by the Lords of Terra and the Inquisitors, by the Space Marines and the Emperor himself? If the stuff that drives the Imperium is built and shipped by mutants, then the purpose of hunting down and murdering those mutants who fight back is an attempt to keep the apartheid system of the Imperium in place, and the normalish people at the top in power, despite the changing genetics of the populace (psykers) and the outward changes that come upon the populace as a direct result of their exposure to the universe. The Inquisition is a terror squad meant to keep the huge mutant population in its place working as unseen slaves, and if they do rise up, to be brutally punished by the powers at large.
Or am I way off base?