Three things make me believe that Thragg would never side with Nolan or be reformed, while I can see Conquest’s potential for reform, but only in a very specific way. These three factors are: 1. Indoctrination, 2. Circumstance, 3. Position.
First, let me address Conquest. While it’s not impossible for him to switch sides since, at the end of the day, they are mortals with brains no different physically from other indoctrinated Viltrumites who have switched sides Conquest’s twisted mind makes it impossible for him to adopt human ways of life. He wouldn’t be able to accept that. While I could see him accepting Nolan or Mark as Emperor, it wouldn’t be enough. Nothing would be able to make him suddenly sane and adopt human values. He simply can’t. So, the only outcome I see for Conquest siding with Nolan is being sent on a suicide mission to fight Thragg, as Battle Beast did. This would allow Conquest to die loyal to the New Viltrumite Empire. There is no outcome in which he doesn’t die in battle, either at the hands of Thragg or after the war by Mark and/or Nolan’s hands, as the new empire would have no need for such brutal exterminators. As for position: While it wouldn’t be as significant as Thragg’s, Conquest is seen as second in strength, with Thragg above him in rank. However, Conquest is still only a veteran soldier just one rank above a regular soldier in the old Viltrumite Empire. While twisted, he is still searching for an heir to follow. Now, onto circumstance: In the comics, Conquest was never put in a situation where he had to choose between loved ones and the Viltrumite Empire, unlike other Viltrumites. Therefore, he has no internal conflict. Additionally, Conquest never lives to the point where Nolan is revealed to be the heir. Even if Conquest somehow survived that long, it would only play out as I mentioned earlier: Conquest would remain loyal in the sense that he fights Thragg and dies loyal to Nolan/Mark.
Now, onto Thragg: First, indoctrination. While all Viltrumites are brainwashed from birth into the old Viltrumite Empire’s ways, Thragg’s indoctrination just like his training and upbringing was much more reinforced than other Viltrumites. While it’s not impossible to break through and reform him, he is, at the end of the day, just another mortal. However, I’ll point you to point two: circumstance. Thragg was never put in a situation where he had to choose between family and the Empire. The Empire is all he had. Even in desperate times, when he had to break his own rules about hybrids and compassion, he never became attached to his children. The compassion he did show toward one of his hybrid children, Ursaal, was insincere nothing more than a tool to be used. He believed that if that was what he had to do in desperate times to turn the tide, then so be it. But to Thragg himself, he never cared for any of his children. He didn’t show any emotion when he ordered them all to charge to their deaths against Mark and the others. Finally, onto position: Thragg, as regent and de facto leader of the old Viltrumite Empire, places pressure and expectation on himself to be the embodiment of the old Viltrumite ways. This makes him inflexible to the idea of acceptance, surrender, peace, coexistence, etc. Therefore, Thragg would rather die than accept such individuals as Nolan or Mark as his Emperor, even if they are of the royal bloodline.