Sorry to keep an argument going, but I have to disagree with Deek's statement. Chaos is not made up of evil. Chaos is the epitomy of randomness, it is everything. The only reason it is evil is that people mostly have some kind of dark side, which feeds the negative aspects of the Chaos Gods. The big 4 therefore are evil, but that is due to the darkness that all mortals harbor within them.
The Imperium is definatly one of the most evil groups in existence. The original intentions of the Emperor may have been good, but the High Lords have screwed that up.
Even if Inquisitors do not take pleasure from genocide (which, lets face it, they probably do), they probably get some measure of satisfaction from it, which is just as bad.
Also, I fail to see how a crusade against the "evil" of alien races and mutation can be seen as defending themselves. The best defence may be a good offence, but the Iperium take it too far.