Feel like I actually want to step in with a proposal here. No idea just how workable this is, but at least it vaguely resembles a plan. Feel free to make something better.
Impact energy is likely somewhere around 5 megatons at worst (including reducing for air resistance), possibly down around 1 megaton, depending on actual physical size. Still bad, but not world-endingly bad.
Akane has the strength to at least slow it down to a survivable level, but not the leverage to apply that strength.
So, crazy plan:
Timestop and zip around to below the center of Walpurgis city. Participants: Sayaka, Kyouko, Akane, Homura
Sayaka creates a platform for Akane to stand on. Kyouko creates a web of chains to distribute the force against the underside of the city. Akane pushes up on Walpurgis city.
Platforms and chains will likely have to be constantly and repeatedly created as they're broken during the fall. However even a few hundred should still be manageable with the cleanses we have left, letting Homura handle that while Sayaka focuses.
If the city's size is about a half kilometer across, then Akane has to push up with the energy equivalent of about half a kiloton of TNT per second to counteract gravity. Considering her punches can atomize skyscrapers, that seems within the realm of possibility. It's just a matter of whether Sayaka can support her.
It might help if Sayaka can layer the platforms in a flower-like pattern, to help distribute the force they need to support as they progress downward.
Meanwhile, those still topside gather and protect the civilians, as the city is crumbling. Ran's speed should be very helpful in collecting people. Ako might also consider using her sonic powers to pulverize an area of the ground into a soft dust that can help cushion the impact of the fall.
Too bad we don't have two Akanes, as the second one could knock off chunks of the city as the civilians are evacuated from it, lowering the weight of what needs to be supported. Though if the city continues to collapse, that may be redundant.
Simplified vote:
[x] Sayaka, Kyouko, Akane, Homura gather underneath the city to counter its fall using Sayaka's platforms and Akane's strength.
[x] The remaining Tokyo girls gather civilians and create a safety area topside.