So the Zaith'isk gives her a rather significant permanent debuff of -2 Con, -2 Int and -2 Wis.

Why is this a problem?

The player has been taught since the beginning that death is meaningless. Characters can repeatedly die or be "lost forever" in chasms but they can always be brought back in full strength with a simple Revivify scroll or by Withers for petty cash. When the zaith'isk cutscene was playing I was literally thinking "it doesn't matter if she dies, I have 10 Revivify scrolls in my pack". The complete disconnect between gameplay mechanics and narrative is something that pops up in BG3 often. Characters can be Disintegrated without any permanent debuffs, but somehow this time it matters because there's a cutscene where someone gets a little bit hurt?

Narratively, you have to let it go far because otherwise she, still a zealot, would just be mad you interrupted the process and messed it up. And what do you know of Githyanki machines anyway? Lae'zel always approves when you let her deal with Githyanki stuff independently. And she needs to learn the hard way for her eyes to open. Unfortunately, this mechanically gimps her value as a party member. So the player is being punished for letting her story arc play out in a logical way. It mechanically encourages you to dump her for Karlach who hasn't been nerfed. What doesn't kill you makes you weaker, eh?

Finally, the game fails to notify you that her abilities got permanently weakened. There should have been pop-up windows after the cutscene saying -2 Con! -2 Wis! -2 Int! Or at the very least some visible condition where conditions normally are. This major ability score reduction was done very much in secret and it sucks to find out about it much later. Personally, I only noticed after hours of playing and finishing the entire Creche, which is extremely annoying.