I'd even have Omni-Man slowly probe the Guardians, asking them some polite questions where he tries to gauge whether or not they can be assets or enemies to Viltrum when they get to Earth, like would they accept an absolute ruler if said ruler gives everyone social security and no one ever goes sick or hungry ever again. Originally, Nolan plans to use the Guardians as breeding stock to mate with Viltrumites, but he drops the plan when he realizes that none of them will accept Viltrumite rule despite all the blessings it can give to humanity. This would then lead to the even where Omni-Man massacres all the Guardians, and it would happen just like in the show, with him fainting after decapitating Immortal being the season 1 ending, and season 2 begins with the fallout from the Guardians' massacre and people believing Omni-Man's story that someone tried to kill them all.
That way, the deaths of the OG Guardians would mean more once the viewers got a whole season to learn about them, accept them, and like them, so when the new Guardians show up to replace them and suck at the job, we understand what Cecil is thinking when he treats them like kids, because they're kids standing in the place of titans. Season 2 would then have its final battle with Mark and the world realizing Omni-Man's duplicity, but then Omni-Man rebukes his son by saying that Viltrum recently sent him a message saying that if the Earth doesn't bow to their rule in 3 weeks' time, the Viltrumite fleet will arrive and annihilate the planet, and Omni-Man killed the original Guardians to make sure that there would be no threat to Viltrum's occupation of Earth, and no reason for Viltrum to deal with humanity harshly. Nolan even says that he got Grand Regent Thragg to agree to rule humanity with a gentle touch, so long as the nations of the world surrender to Viltrum peacefully.
Season 2 ends with the world surrendering to Viltrum as Thragg arrives with the Viltrumite fleet. Omni-Man and Invincible welcome him along with Cecil and the Global Defense Force, handing over a flag of surrender in the UN building, with the world leaders present and bowing. Thragg accepts Nolan's surrender, thanks him for a job well done in bringing Earth and humanity into Viltrum's fold. Thanks to the fact that the human governments surrendered without a fight, Thragg allows them to retain their power and continue going about their business, so long as they acknowledge Viltrumite rule, and he also shares Viltrumite science and technology with the world leaders present. Nolan goes home to Debbie and Mark, and he starts drinking heavily, the losses of the Guardians having affected him dearly, saying that they were his friends too. He goes between justifying what he did because it was to save humanity, to him having nightmares of the old Guardians accusing him of murder.
Season 3 would be a mix of some people trying to resist the Viltrumite rule, while the new Guardians continue to fight against increasing supervillain threats, with increased Viltrumite support. People would also be adapting to Viltrumite rule. Eve's father, for instance, tells Eve that there's no need for her to go off being a superhero when the Viltrumites are doing their job for them. Nobody messes with Debbie at her job because her husband is a Viltrumite. Mark gets letters of recommendation at school because some high-class schools want to get in good with their new Viltrumite overlords. The other Guardians are split 50/50 on the Viltrumites; some like Rex like fighting alongside Viltrumites and even tries to score with a Viltrumite woman, others like Robot don't trust the Viltrumites since they cause too much damage, while Monster Girl and Dupli-Kate couldn't really be bothered to care so long as the Viltrumites help them fight supervillains.
Immortal comes back and tries to rally an underground resistance against the Viltrumites, but Cecil and the GDA oppose him, since not only is Cecil trying to keep Thragg happy, but Viltrumite science and technology has eliminated world hunger and diseases. Not to mention that the GDA now has more Viltrumites on call to squash any supervillain resistance. But instead of the villains disappearing, they escalate; they become more powerful and double-down on resisting the good guys and the Viltrumites, and this gets more people killed.
Neither side is portrayed to be completely good; the pro-Viltrumite side ignores the fact that Viltrumites don't give a rat's ass about collateral damage and they send GDA soldiers to kill any human who tries to rebel against Viltrum, while the rebels also don't care that their actions cause collateral damage, and some even target humans who befriended Viltrumites, like say, some rebels try to kill a woman that a Viltrumite is dating. That way, Mark still does his superhero stuff as Invincible, stopping villains and saving lives, and Omni-Man helps on the side, but you have a gray conflict of rebels vs empire that isn't so black and white.