I mean, she spent several centuries doing exactly what Calyx needed of her, and 7.2 showed us that Calyx is a 'learn from failures' kind of person more than he is a 'plan for all eventualities' person. Why throw her out if she's doing everything needed of her, and the event that she goes against him both hasn't happened yet and, as far as they know, very well might never happen? That just sounds like a whole lot of needless work to produce a perfect plan that you don't need, because the current one's already working just fine.
And similarly, why go through all the effort to use the regulators to manipulate people's memories to achieve a plan without Sphene, when 'get Sphene to ask someone to do something' has worked for hundreds of years? Hell, I'd argue that the existence of Oblivion and the largely-undiscussed people not using regulators shows that trying to change their approach is really not feasible; he actually can't control the memories of the entire population. However, both Oblivion and the non-regulator-using masses seem to like Sphene well enough, at least as far as they ever could like someone in her position, so why would you ever stop using her as the figurehead and risk escalating them into action? You call the idea of Calyx replacing Sphene 'pragmatic', but I actually think it'd be the mark of an irrational and paranoid actor to replace something that's worked perfectly for centuries simply because, in some unforeseen circumstances, it might backfire. Especially because there's absolutely no guarantee that your replacement plan works any better, and that the act of replacement itself could very well cause great issues.
I don't think it's that 'the writers didn't think of this' or anything: I think they absolutely did, and you're reading Calyx as a different sort of villain than he actually is. He's not the 'all according to keikaku' elaborate mastermind that calculated for every possibility that Quickthinx Allthoughts or Emet-Selch claimed to be. No, he might actually be scarier: he's a calculating, scientific mind that learns from mistakes and tries again. Endless Sphene eventually failed him, so he made a new Sphene that did; the lightning bolt didn't work, so he hit us harder the next time. Which has the potential to be genuinely terrifying as a villain, because as long as he himself can walk away from things, he's never 'failed'; he's just got more data for next time.