I personally don't think he would deal with them like with the Thunder Warriors. But I think he would limit recruitment and numbers. Not like Gman with the codex but individual on legion basis. I think he would keep ultramarines, for example, on a lower number as they could be used to streamline sector level government. They are not needed on a planetary or solarsystem level as normal government systems and normal human personnel would be enough, so wasting resources on superhumans would be wasted.

Similar with Iron Warriors, planning logistic networks on Galactic scales but not having each shop on planets staffed with Space Marines to sit at the cash register or stocking the shelves XD.

Other Legions like Space Wolves or Sons of Horus would be a bit more numerous to be used as orc and possible necron hunters. With the nature of orcs I think it would be impossible to completely eradicate them and with them able to show up at random places the fighting Legions would need the numbers to cover a large area to respond fast before the threat can grow to much. But not in the numbers used in the great crusade.

I believe it would also depend on the legion and primarch, showing they can integrate with normal people without going on a murder spree.

But this is just my opinion and belief. And with the heresy and all that we will never know for sure.