He’s taking his competence and experience with him, for starters. Transitions always take time for the newbie to get accustomed. There’s also some public image effect to a respected veteran an expert disagreeing not just behind closed doors, while outwardly being seen as another asset of a regime they no longer support, but out in the open, at the expense of losing their job. They might not be allowed to publicly speak out against their superior (insubordination), so by quitting, they explicitly cut that chain and avoid the consequences (which would involve being fired at the very least).

We don’t know how long and how much he has tried to fight back from the inside, how much good that might have done, and how much pressure he has faced. It’s possible he was slated for replacement anyway, and given the choice between being fired and burning the bridge himself, he felt the latter would send the stronger signal: “I hate my job so much that I’ll quit because I can’t stand to wear this title while that snotrag up there is dripping all over it. Fuck this shit, I’m out.”

And it might also send a signal to those working under him that respected him: You shouldn’t cooperate with this shit.

(There are less charitable explanations that might apply to this guy in particular, but the above generally holds for officials making a point of quitting their position)