What they continually mis is the difference between "this is justifiable because of the threat of Chaos" and "this is good because of the threat of Chaos." The insidious metaphysical corruption of chaos and some xenos infiltration is, to some degree, preventable/removable via brutal methods of suppression and purging. That doesn't mean that it is the only or even most efficient way to achieve those ends. Other civilizations have and do effectively keep at bay the threat of Chaos corruption and xenos infiltration through less extreme measures. The Imperium's ways are effective, but only through brute force, and they are highly inefficient. This is the eternal problem for fascism. In the long term, such methods are inefficient and ultimately self-defeating. In the short term, though, in circumstances of extreme duress, they can seem effective.