Since malleus inquisitors basically dedicate themselves to fighting daemons and warp monsters, and since the warp is known to 'change' you somewhat on contact.
Couldnt it be reasonable to assume that most malleus inquisitors inevitably develop some form of mutation in their careers, an extra finger here, another eye there. It would rly be an occupational hazard.
Bearing this in mind, how could the inquisition realistically abhor mutation when in all likelyhood they will wake up one morning with one themselves!!