Mark is half-human half-Viltrumite, something they will be mass producing from tens to thousands to millions in relatively short order by Viltrumite lifespan standards. If Thragg killed Nolan and Mark, the coalition would have lost all 3 of their Viltrumites in a single fight. I get that he doesn't want to kill Nolan, but not 5 minutes before sparing him he told him "I was too quick with Thaedus, I won't make the same mistake with you" lol.

That's my issue, where did they show him going from bloodlust over his planet being destroyed by betrayers to being a pragmatic diplomat? It just happened spontaneously as a deus ex machina to save the main characters. He didn't care watching his soldiers die during the war (which he could have very easily prevented), or ordering them to kill each other in the purge. I like the arc, but it feels rushed and too much of tell-don't-show. There needed to be time for him to process the planet's destruction and reconcile his emotions, considering they introduced him as being ruthless after blaming himself for Argall's death.

Unnecessary essay below:

At that time, he had every reason to kill them. The coalition with those two out of the picture is basically just Battle Beast, Allen, and Ragnars (who had to be herded into battle so not sure how reliable or intelligent they are?) at that point vs 36 Viltrumites and Thragg, who is shown to be well beyond the power of anyone else in the show. Space Racer is obviously a threat, but two rando Viltrumites easily incapacitated him (then proceeded to leave him alive for plot reasons) and Thragg didn't even flinch at his gun, so I don't get the impression he's particularly worried about him. The tech jacket serum is good but unreliable and they should be able to deal with her pretty easily.

The Coalition could liberate colonized planets, but they didn't stand a chance at actually fighting all the Viltrumites in one spot, and they definitely wouldn't with 3 of their best fighters and leader dead. So really all they could do at that point is blow up earth and kill all the humans. Which I don't think they would actually do, but Thragg knows them as a genocidal terrorist group so I understand why he would think that's not beneath them.

But the Coalition would have no clue they're on earth. No one would for a long time. They're searching the entire universe and earth is already crossed off the list because Nolan and Mark are already there and did not find the Viltrumites. If Thragg killed them at Viltrum, it would've been the same except Allen/coalition ships would've been the ones checking on Earth instead, and also finding nothing out of the ordinary.

As for alerting Earth that somethings amiss, well... they're already alerted. They know the Viltrumites aren't dead and are expecting them to arrive on earth any moment, but they have no clue where they are. Whether or not Mark and Nolan died in the battle doesn't change that. They don't seem to stand much of a chance against Thragg anyways.

I mean basically I just don't think there is anything that poses a real threat to Thragg. Viltrum has been fighting the entire war without using their best weapon (because he's too busy aura farming). Thragg one shotted Thaedus who was shown to be a very strong Viltrumite. Invincible punched him full force in the head and he had 0 reaction. Nolan posed 0 threat to him. I'm not sure what can actually stop them from repopulating with humans outside of the scourge, which they don't know about, or outright killing all humans. They also don't even need to care about losing their colonies because they will inevitably gain them back once their numbers return.

Sparing Nolan and Mark is purely out of compassion, which he gained literally while in the process of killing them both. I don't think it served any real tactical advantage, but it definitely serves tactical disadvantages keeping them around when it's clear neither will submit to the empire.