Yep, no one, not even the High Lords themselves are above the remit of the Inquisition. Though they will need a significant amount of support and/or influence to do anything extreme and actually succeed in doing so. Astartes are just as likely to ignore an Inquisitors request as they are to follow it however, depending on their relationship.
Key example as ever being the Space Wolves, of what can happen if an Inquisitor attempts to exert his authority over the Astartes without fully comprehending the fallout of such actions. The Wolves utterly disregard the Inquisitor in charge of the cleanup and fallout of the First War for Armageddon, actually killing him in the end as well as several Grey Knights with him, including a Grand Master.