It wouldn't be legal to use him as your only HQ choice but I don't see any rules preventing you from using him as an ally in a Daemonhunters army. You wouldn't be allowed to add any henchmen to Karamazov - he's a special character and comes 'as is'.
Also it would only be legal to give the Witchhunter henchmen to a Witchhunter inquisitor - no mixing and matching between codeci. However you could use the models if you prefer the look of the witchhunter henchmen - just make sure that you use the rules from Daemonhunters if you have a Ordo Malleus inquisitor.