IIRC, Waller is currently persona non gratis in the government since she was outed by Adebayo. Also, Waller probably has a lot more protection via blackmail material on powerful people than poor Chris.
But beyond that, yeah, I kind of feel like Rick Flag Sr.’s character has been all over the place if you actually compare him from Creature Commandos to Superman to Peacemaker. There was just too much about that last episode that made zero sense to me. Like, I get that he’d make a deal with the devil regarding Luthor. But then becoming Buddy-Buddy with Luthor’s cronies? To the point of “Hey let’s celebrate and get drinks together?” Wanting to use the portal only as a prison for metahumans? - which is funny because Peacemaker isn’t even really a metahuman. I know Economos made the whole “when have the powerful people ever cared about common people” point. But even then, it’s an entire world filled with resources that are just being wasted. I know it’s comic book logic but even then it kind of strains my brain a bit. It really felt like all they were doing was setting up a future plot point for another movie which honestly, that’s the trap the MCU fell into. It worked until it didn’t work.