I don't see how that justifies anything, because the Cataclysm is absolutely a direct intervention, so any concern about no direct influence is clearly misplaced. Once a decision like that was being discussed, the only good act would be to directly intervene in a way that did not cost so many lives.
But, it's a direct intervention by the Pantheon, not any single god. So, it keeps the notion that the gods don't take a direct hand. And, since half the gods are evil, the pantheon as a group, can certainly do evil things. The good gods tried to stop it but failed.
Note, gods granting spells was always a bit wonky in AD&D. 1st and 2nd level spells were automatic. It wasn't until 3rd level spells that you needed a god to grant the spell.
But, in any case, since we're changing canon, there's no reason to hang onto how things worked back in the day. This isn't trying to justify how it was done then, it's trying to find a way forward that works now.
BTW, though, other gods granting spells is absolutely a thing by 2e. Forgotten Realm's Faiths and Avatars talks about various heresies where clerics are still being granted spells (in a setting where the gods are a LOT more directly active) but, there being some question as to exactly who was granting those spells. This isn't something new.
So, no, granting spells isn't really directly intervening, again, because everyone can do it equally. A priest of an evil god gets the same spells as a priest of a good god.
In any case, can we at least agree that there needs to be a Cataclysm at all? Because, I'm getting the sense here that people are arguing for the removal of the Cataclysm entirely and that's a bridge too far for me. That changes the setting too much. No Cataclysm and the ensuing fall out and Krynn stops working as a setting.