Cecil is morally bankrupt and always has been, he's also just doing his best, but he absolutely wasn't correct.
Long winded character study of my favourite man, Cecil Stedman, incoming.
Cecil spends all of season 2 manipulating mark and lying to Debbie and ppl still think he was genuinely justified in what he did to mark in season 3.
Through season 2 Cecil assures Debbie that Mark calls the shots, sets his own schedule and that Cecil isn't making him do anything.
Cecil assures mark he isn't his father and shouldn't be burdened by Nolan's actions, but the second that mark shows his own agency, the second Debbie cannot hear him, Cecil tightens the leash on mark.
"you're not your father, mark." becomes "that's exactly what your father thought." when he doesn't like Mark's initiative to save the aliens. Mark is leaving to try and save lives, and Cecil compares him to Nolan because he doesn't want Mark to go. That's straight up manipulation.
"he sets his own schedule, I don't make him do anything he doesn't want to" to Debbie becomes "you work for me, mark." When Debbie isn't around to say otherwise. Once again, he's taking this teenager's blind faith in him and trying to leverage it the way he wants.
These are quotes from Season 2 when Cecil and Mark's relationship was good! This man is passively manipulative, always looking for the advantage and always playing victim.
Another super important lie to keep in mind when considering Cecil's character is where he gets the corpses for Sinclair. He assures Mark that they were donated, but we know for a fact they're just stolen military men "serving their country one last time". That's what Cecil says in season one, and we know that those soldiers didn't consent due to the timing of the season.
Beyond that, Cecil's actions in season 3 have been nothing but cruel and manipulative. FEELING threatened by someone and BEING threatened by them are not the same thing. Cecil has every right to feel threatened but up until the Reaniman grabs him, Mark doesn't threaten Cecil.
Cecil spends that entire interaction exacerbating their interaction. Showing mark how many Reanimen he's surrounded by does nothing to lower tensions. THAT is a threat! Especially after he sent the first wave after Mark.
Knowing everything we know about Cecil I am confident in saying that even his admission of fear (while based in reality) was another attempt to manipulate Mark into giving up the argument. Guilting Mark into passivity rather than explain properly why Cecil is doing the things he is.
Mark crashing through the ceiling was a justified end to their conversation when you consider that mark is surrounded by enemies on the ground and no longer knows where he stands with Cecil.
Cecil changing his tune from "go home, mark" to "you're coming back to the GDA with me" is a VERY concerning development when you consider that Cecil spent far more chasing mark down than he would have spent fixing mark's temper tantrum.
Mark thinking Cecil was going to kill him wasn't just a valid thought, it was a totally rational one after Cecil has proven that when Mark isn't a good boy who does what he's told, Cecil will see him as just as vile and evil as his father, no matter the reason Mark disagrees with Cecil. Every prior interaction they've had Cecil has only proven that.
TLDR: Since Nolan left, Cecil has been working overtime to take advantage of Mark's broken reality and less than stellar sense of self. Cecil's long list of lies and manipulations have had an adverse affect on Mark, and have actually pushed him away rather than putting him under thumb. The fight and crashout wasn't commentary on Mark (who was acting like a betrayed and hurt teenager) but commentary on Cecil, who is making terrible, shortsighted choices because he's losing control of a situation.
Also sidebar; The reason we can accept batman keeping kryptonite is because we know he won't use it unless absolutely needed. He's a patient, thorough and diligent character who is unshakable and reliable in most continuities of his story. Cecil doesn't and shouldn't have that same leeway, being as flawed a person as he is. Cecil is a bad person on the right side of history within his canon, but bad people make worse choices and we're seeing that perfectly this season. It's so crunchy I love this show so much.