Because it was purged of its taint, and the Inquisition knows better than to mess with the Wolves of Fenris at this point.
When he took the axe Logan Grimnar fought a battle of wills with the Daemon Axe, and won. The Old Wolf fought Chaos in a staring contest, and made Chaos double down. He's THAT badass. But to be sure it would not corrupt the people around him he had it reforged to purify it of its taint and make it usable without the threat of Chaos.
After this there was the First War of Armageddon, which ended up with the Grey Knights and the Inquisition going against the Space Wolves. The Inquisition and Grey Knights took notable losses, and further more a shift within the Inquisition took place. Old Man Logan wrecked faces left and right, forcing the Inquisition to be more compassionate and not so purge-happy lest the Sons of Fenris come and beat them so hard over the head they poop their own skulls. If anyone else had done this they'd be branded heretics and be excommunicated. But not Logan Grimnar, and not the Space Wolves. They commited open treason and got away with it, because nobody wants to start a second Horus Heresy.
And even if the Inquisition did start to fight them, who would join them? Sure, the Imperial Guard might work, but what Space Marine chapter would fight the Space Wolves for being compassionate and standing up for the plight of the common man? No First Founding chapter, not even the Dark Angels, would do that. And if they drag along all their later foundings, you will have a massive reboot of the Horus Heresy, with all Space Marines against the Inquisition, the Grey Knights, the Minotaurs (who are on the side of the High Lords of Terra) and various other smaller armies.
Nobody wants that of course, so the Inuisition and the Space Wolves made something of a deal: the Inquisition would tone down their jerkiness and the Space Wolves would not cut off their heads.