Assume the theoretical end goal is dewitching being cracked, and creating some alternative to clear seeds that doesn't rely on witches, which we are capable of distributing to every magical girl in the world. That's not the only possible outcome but it seems like what we're aiming for if we want dewitching to be a practical thing.
What I'm personally looking at for a theoretical end goal is not just de-Witching, but also de-Contracting.
This is the comprehensive solution to everything Kyubey has engineered and the ultimate answer any problem caused by magical girls. The complete system breaker.
Girl about to turn into a Witch? Break their contract. Girl feel like they're no longer human and want out? Break their contract. Bunch of magical girl serial killers? Capture them and break their contract; the only way they can continue causing trouble then is by mundane means and then the mundane justice system gets to handle them. Much cleaner than ripping their Soul Gems out of their bodies and stuffing them in a freezer or trying to contain them as a magical girl and hoping they don't Witch out or blow their Soul Gems up in a Kyoko-style kamikaze attack.
Even if somehow they can be prevented from ever turning into a Witch, magical girls live forever and they are functionally immortal.
What this means is, in the long-run, the world will end up with severe societal issues given there's a ton of them walking about with zero restrictions on magic use. Human society will become a two-tiered segregated system - on the lower strata, you will have the mere mortals, unpowered and uncontracted and then above them, the undying superpowered demigods who will never die of old age and whose only possibility of being killed is by breaking a small golf-ball sized Gem which is almost always hidden on their person when they are transformed in combat - possibly meaning always all the time if they have no reason to worry about running out of magic - and thus also protected by the same superpowers they wield. Even if they tried to self-police, the inevitable conflicts between the ones who disagree would cause untold amounts of damage to everyone else (see: the Sendai Civil War).
Not a very fair world to live in. No matter what anyone might say about the real world being a terribly and unfair place, at least death (and taxes) comes equally for everyone. And this is not even getting to the part where only females get to contract to begin with and you are automatically screwed out of superpowers by default if you happen to be born with certain bits in between your legs.
Ideally, even if nobody could stop girls from making a contract, the world should at least have the option of rescinding the privileges gained from those who are deemed to have abused it. In lieu of that, there really isn't much of a middle ground between ripping their soul out and refrigerating the body and simply letting them go. Because if they don't want to get caught they will either end up a Witch or blow their gem up in a blaze of glory, which is essentially ripping their soul out except without preserving the body anyway.
The issue with the Meguca system is that its fueled BY magical girls becoming witches. At some point Kyubbey when he first arrived made a girl into a magical girl in a world WITHOUT witches. She become witch number one and was then hunted by magical girl number 2 who becomes the next witch and so forth.
Well you know, at the end of the day it's fuelled by Kyubey. That second magical girl wouldn't exist if he hadn't found her and gotten a contract out of her.
Would that first Witch have have been able to kill off everyone in the world?
Not the world as it is today, I don't think. We know for a fact that Homura's mundane weaponry works perfectly well on Witches and it is possible for strong enough individuals (i.e. potential magical girls) to survive for at least a while in a labyrinth without getting Kissed or brainwashed by a Witch.
In theory, an organisation of such "potentials" armed with high powered mundane weaponry could defeat most Witches that aren't Walpurgisnacht, albeit probably with a nasty casualty rate. Even if every existing magical girl were to suddenly turn into a Witch, as long as that Witch was only a "normal" Witch and not as strong as Kremhild Gretchen or Walpurginacht, I'd argue humanity would have a fair chance of surviving.
The problem is that Kyubey keeps on soliciting contracts and constantly makes more and more of them all the time.
And wipes the memories of anyone mundane who might organize such a resistance, apparently.
