Not going to defend the shit writing, but the reason behind Sylvanas going all genocide was to send as many souls as possible into the Maw, as that would fuel the Jailer's powers.
Everything that died after the end of Legion (when Argus' soul broke the Arbiter) ended up in the Maw.
But other than that, yeah Sylvanas apparently never saw it coming that the evil big bad in evil armor and wielding a magic called DOMINATION wanted to enslave people.
There's been a theory floating around that really they'd planned for a twist that the Primus would be the big bad behind the Jailer, but they supposedly had to scrap it when they decided to cut Shadowlands short. There's quite a few arguments going for it actually, and it does make the lore a lot less stupid if that's the case.