Ordo Malleus and that unusual potrusion!

I think it depends on the experiences of the Inquisitor. Yes, there are puritans, but as someone else said, with the very generic Caesar/Batman quote "Either die a hero, or live long enough to see yourself become the villain"... It all boils down to experience. The inexperienced Inquisitor can say "Chaos is EVIL, the warp is EVIL, anyone using either to further their own agenda, or even the Emperor's is EVIL"... but, the problem is, the Imperium is rife with contradictions. The Astronomican uses the Warp, Librarians and navigators, and even sanctioned psykers can be used to fight Chaos (though the last one gets shot by commissars quite frequently, like Kenny from South Park).

Add to this, studying Chaos begins with studying the signs of it. Eventually, an Inquisitor will deign the need to study the people who use Chaos. Find out what makes them tick. Much like a detective who has to get inside the mind of the criminal in order to comprehend his motives, which will point to where he will strike next. And with enough experience with the humans summoning these daemons, the Inquisitor will need to study the daemons to understand what makes them tick. Eventually, this study goes outside the bounds of reading studies already performed to reading heretical grimoires of excommunicated Inquisitors, where the book must be procured through a long and difficult process, and the Inquisitor will need a very damn good reason for it.

Eventually, the accumulated knowledge will tempt the Inquisitor to actually commune with a daemon, to learn a morsel of knowledge pertaining to an upcoming Chaos subversion. He/she will begin with a daemon whose true name is known, confirmed and verified throughout several forbidden as well as official texts. Then, with confidence growing, the subsequent summonings will increase in what kind of daemon is summoned.

Power corrupts, absolute power corrupts absolutely, some might say. However, I say, as much as I just laid out all that, it is also highly likely that such a chain of corruption could be staved off for a few hundred years, and that the Inquisitor in question might only have gotten to the part where he/she is reading about what the daemon he/she just fought was, how it was summoned and what its true name is... before said Inquisitor dies in battle, or from old age.

At any rate. The taint of Chaos doesn't get everyone. It's why Horus fell, but Rogal Dorn didn't. It's why half the Inquisition works for Chaos unwittingly, and the other doesn't. I won't say it's a surefire bet that every Inquisitor will be corrupted, but I will say that given enough time, everybody's survival rate drops to zero.

The first Inquisition was founded with the express purpose of preventing another Horus Heresy. The men and women at that time did not, nor could they forsee how far down the rabbit hole the Imperium would go, nor could they have anticipated how strong the cult Imperialis would become... The first (chronologically) mention of the Inquisition I can think of is at the end of the Flight of the Eisenstein, where, at the end, one of the characters is approached about joining an organization to investigate and eradicate future rebellions.

The whole notion of purity is a canker in the mouth of the Emperor. It is a sore on his foot. The Emperor sought no worship, and cut down those who praised him as a god. Admittedly, the whole repulsion of daemons by Keeler suggests that there's something about His name... but, even so. The Emperor was a powerful psyker. More powerful than any other. How do we know he can't reach out across the galaxy when He's needed, by the strength of his power, not by virtue of divinity?

Regardless, the Inquisition might appear to lack the moral fiber to do its duty, but remember, the Inquisition has to have a questioning approach to everything, even itself and the Emperor, or else it won't be able to root out the heresies, daemons and xeno before they conquer mankind.