Lyta did blow up a planet, refused to take responsibility for it, and implied she was a Manchurian Candidate... and then proved she was, like, a month later.
Sheridan doesn't like being lied to or manipulated, especially by people whose actions he's responsible for. It comes up repeatedly. He gives Stephen essentially the exact same "Never, ever, ever do this again or I'll have you shot" speech after he finds out that he'd been running the telepath underground railroad. He sets up a war council in season 3 specifically because he's afraid hidden agendas and secret plans among his allies might cause them to hurt each other.
And destroying Z'ha'dum was a bad call. At best, at best, Lyta was condemning a hundred innocent people to a living hell of endless hunger for the Machine because one of them had the misfortune to draw the affections of Al Bester, and she was willing to hurt all of them to hurt Carolyn specifically, just to use the suffering of that innocent person to hurt Bester. That'd be bad enough, but there's a straight line between the destruction of Z'ha'dum and the Drakh taking over Centauri Prime, so that's thousands of people dead in the raids and subsequent war, and millions in the bombardment and the eventual detonation of the Drakh's hidden doomsday bombs when they were driven from the planet. It's an open question whether, if they'd been able to stay where they were, they'd be so motivated to destroy the ISA as to attack Earth and Minbar, but let's be generous to her and say they would've anyway.
Lyta did an incredibly shitty thing for petty, vindictive reasons (or she's not in control of her own senses and judgement, which isn't better), exploited Sheridan's trust to do it, and didn't even imply she'd stop doing things like that. Yes, if you say, "I don't work for you, I do what I want, try and stop me," you don't get to be all shocked Pikachu when you find out you weren't added to the payroll without even asking for it. Crediting that to anti-telepath bigotry really removes all of Lyta's agency in overtly asserting her independence and very much not trying to be part of the family.