The original illithid empire was destroyed after mother Gith made a pact with Tiamat, so also via indirect divine intervention. Vlaakith doesn't know how they did it, but (some of) the Gods will have this knowledge still and might be able to reuse it, to prevent a new grand design from swallowing up too much of their domain. (IMO)
Orin, Gortash and Ketheric still had to deal with Orpheus and the artefact. A thing which does not needs to bother Tav. But Jergal, Mystra and other Gods. Shar, for example, who must feel a bit offended, are unlikely to let you do your thing.
Imagine, Jergal struck your name from the archives during the adventure, but could then just as easily undo that, and boom. You're dead.
I'm pretty sure that straight-up eliminating mortal, material creatures, even extremely powerful ones, is a pretty big no-no in the divine playbook with different explanations as to why in any given setting or campaign, otherwise you'd just get entire races, civilizations and power-hungry beings simply getting deleted non-stop perpetually and eventually a second Divine War as they run out of minions to slay and confront each other openly.
In some settings, deities don't do that becase Ao will bitchslap them if they do. In others, they simply don't have the ability to exert such direct influence outside of their own domain, especially into the Prime Material. In yet other settings, there is a treaty between most Deities to keep their hands off Prime affairs, sort of like the divine version of mutually assured destruction, as to not get into an apocalyptic divine war.
Neither Jergal or Shar should be able to touch you while outside their personal domains, only send their followers to do so. And if you can escape into Illithid-space, then their followers shouldn't be able to do much about it either, or else the Illithids would've been destroyed long ago.
Ao also specifically put the gods in charge of souls. And as Larian invented that ilithids don't have souls it would mean Ao would turn a blind eye to the Netherbrain getting blown up by the gods.
And as others already said, Faerun is swarming with high level characters.
We are stopping that entire plot at lvl 12, imagine what lvl 20+ characters can do.
Mind blank, teleport, start throwing around wishes and meteor swarms.
They made a pact with Tiamat, sure, but once again it was certainly not Tiamat herself who fought the Illithids, she only lended the red dragons, who are essentially her flesh-and-blood mortal followers to the Gith, same as any other deity's modus operandi. Ao will absolutely not turn a blind eye to deities going out of control against something or someone just because it's 'soulless', there are plenty of monsters, constructs, and even sentient beings in DND who canonically don't have a soul and that never gave Gods the carte blanche to just delete them from existence as they please.
Ao is much more than an appointer of soul caretakers, if you really want to dissect Ao's theoretical personality from the lore we know, then he would more or less be the personification of the DM - an arbiter of fairness ensuring that certain beings like Gods aren't too 'OP' and don't pull off too many 'Deus Ex Machina' stunts in the realms.
As for the whole 'hero' thing, it's pretty much a moot discussion, already said everything there is to say about it and everybody ignores the existence of Illithid-controlled space for some reason. Why didn't 'high-level heroes' just kill off all the Illithids agaes ago? Why do heroes have the ability to lose in the game? Why do heroes have the possibility of TP'ing in campaigns and playing through a dark timeline where bad guys took over instead of new heroes doing the job instead?
Yes, there will be heroes. But it's going to take much, much more than even your average high-level party or lore folk hero to defeat the Netherbrain IF the netherbrain actually unifies the Illithid race behind it and pulls back to the Far Realm/Illithid-controlled space to execute The Grand Design.
