I wouldn't ditch it, just make it that failing once doesn't lock you out, give players options to go further if they fail one Persuasion check. Many tables (not all) don't make it that you fail your goal immediately for failing one roll, so I don't think the game should either.
Part of the issue is that in tabletop games you can come up with ideas to recover or try other things to get what you want.
In a videogame that isn't possible - only pre-scripted routes exist, and if you fail the necessary rolls for them you are locked out forever.
I don't think there's really a way around this. Sure, they can script extra routes, but that's a ton of writing and scripting, and you're not really accomplishing the core
of what makes that work in tabletop (because players can't really be as creative in a videogame as they can when playing tabletop - they're constrained to whatever options the developers give them.)
Allowing automatic rerolls is silly. You could just make them auto-roll 20, in which case why have the roll at all? The meat
of the 5e skill system - the part that's actually fun and which works - is coming up with clever ideas and selling them to the human DM sitting across the table from you.
This will never, ever, ever be even remotely a part of BG3. It cannot be done currently; there's no AI capable of that. And without that the 5e skill system is a broken, pointless, unfun mess, and will always
be a pointless broken unfun mess without a single redeeming feature to it. It adds nothing whatsoever to the game in its current form and there is nothing in it remotely worth salvaging.
They need to revise it into something that actually works for a videogame, which means ditching most of it and starting over from scratch.