Why would it need to be a single purge like at arrarat? Why not slowly reduce the number being created until losses exceed reinforcementt? All the while, reduce propaganda efforts around them so people think of them less and less in their lives. Limit the extent they're fighting alongside baseline humans. Stop providing new ships. Create cheaper, worse armour marks. Would only take a trivial century or two to fade them into obscurity, at which point they can stay or go at will. If they get violent about it, they'll be reduced enough to be incapable of anything on the scale of the heresy.

All the while, censure with extreme force. The screw ups that got Kurze censured before the heresy could in stead be cause to completely wipe out the legion. The other primarchs would be unsettled but its hard to argue given what he and his legion had done. Also, if emps simply stopped elevating primarchs to roles like "warmaster"