Greif Seeds can't actually be Lost Logia... they are easily replicated. Neither would Soul Gems... the Lost Logia whatever makes the Soul Gems.
Its not that the Puella Magi are imprisoned in their Soul Gem or that they themselves are their Soul Gems... its tht the Soul Gems are their new real bodies. This answers my question about where their self is (the destruction before converting thing) and makes me more certain that relative to DSKS that they are reverse demons. If we look at the Soul Gem's self destructing as an issue of pressure release, Myth Busters proved that over pressured water heaters make anti material projectiles, the issue is pressure release. So your solution is to stop the pressure build up problem. This means in the short term bleeding off the pressure, which is what GS are used for. The long term solution would be to stop the build up from happening in the first place.
As I mentioned before, they need some thing that acts like cast markings in AMG/OMG, the main problem is that SG and GS are fragile. Drilling a hole will shatter it... and the cast marking equivalents would need to be on the SG's themselves. You can transfer by osmosis... but that leaves you with reliing on a a limited use product... the production of which is a large part of the problem of the GWs... which means stopping the production of PMs... or altering SGs so they can't turn into GW... without smashing them all or otherwise killing them all. Homura's wish as I understand it is worded so it can trigger a loop reset in five minutes or in 80,000 years. Glee for the Draconian way to solve the issue.
The other ossmosis method is to toss the SG/GS into holy water. Which will make it go boom. Being infernally based magic and all good enough for GS, but fail on SGs. Though with two priests and the SRLJ around making said holy watter would be cake.
So the next method I can think of is to make a device that will drain off the Corruption and dispose of it. A good way would be to make a Corruption/Anti-Corruption reactor and attach the SG and something to drain the Corruption into... then use the obliterating effect to power a device. In short, use the avaiable tech from DSKS, TSAB, and Moon Kindgdom MagiTech to make the equivalent of an intelligent device with a meat body projection. Its simple enough at that point to either make the device the size of a Babbage Computer running a lan party for 20 people and/or make it so the PM can physically inter act with their own extended core.
Then after a few tech revs, you can have them more and more mobile and the devices themselves more portable until they end up as some odd cross between an intelligent device and a Knight of the Book. There can be a trade off in that they can't maintain a body while their neo-core is in jewlery or combat weapon mode. Plenty of room to muck about with... and as this involves Zeke, a Whispered with training in MagiTech, divine magic, whatever he can get his hands on magic, with Skuld tutoring... its easy to say the kit bashing is so extreme and convoluted that they end up in Zeke's care as he is the only one that can make heads or tails of it. (Zeke would is combining Infernal, Divine, Arcane etc... magics and that is going to leave the TSAB a system or three behind... I'm sure their command structure would love to see taking up priesthood as legitimate field of study as iffy. Lack of Scienciness and all.)
This will allow them as inherited items for Zeke's family, use them as a cautionary tale and have them be around... use them for later stories et al.. You can temper it by having Zeke need to get part from TSAB.
Its not that the Puella Magi are imprisoned in their Soul Gem or that they themselves are their Soul Gems... its tht the Soul Gems are their new real bodies. This answers my question about where their self is (the destruction before converting thing) and makes me more certain that relative to DSKS that they are reverse demons. If we look at the Soul Gem's self destructing as an issue of pressure release, Myth Busters proved that over pressured water heaters make anti material projectiles, the issue is pressure release. So your solution is to stop the pressure build up problem. This means in the short term bleeding off the pressure, which is what GS are used for. The long term solution would be to stop the build up from happening in the first place.
As I mentioned before, they need some thing that acts like cast markings in AMG/OMG, the main problem is that SG and GS are fragile. Drilling a hole will shatter it... and the cast marking equivalents would need to be on the SG's themselves. You can transfer by osmosis... but that leaves you with reliing on a a limited use product... the production of which is a large part of the problem of the GWs... which means stopping the production of PMs... or altering SGs so they can't turn into GW... without smashing them all or otherwise killing them all. Homura's wish as I understand it is worded so it can trigger a loop reset in five minutes or in 80,000 years. Glee for the Draconian way to solve the issue.
The other ossmosis method is to toss the SG/GS into holy water. Which will make it go boom. Being infernally based magic and all good enough for GS, but fail on SGs. Though with two priests and the SRLJ around making said holy watter would be cake.
So the next method I can think of is to make a device that will drain off the Corruption and dispose of it. A good way would be to make a Corruption/Anti-Corruption reactor and attach the SG and something to drain the Corruption into... then use the obliterating effect to power a device. In short, use the avaiable tech from DSKS, TSAB, and Moon Kindgdom MagiTech to make the equivalent of an intelligent device with a meat body projection. Its simple enough at that point to either make the device the size of a Babbage Computer running a lan party for 20 people and/or make it so the PM can physically inter act with their own extended core.
Then after a few tech revs, you can have them more and more mobile and the devices themselves more portable until they end up as some odd cross between an intelligent device and a Knight of the Book. There can be a trade off in that they can't maintain a body while their neo-core is in jewlery or combat weapon mode. Plenty of room to muck about with... and as this involves Zeke, a Whispered with training in MagiTech, divine magic, whatever he can get his hands on magic, with Skuld tutoring... its easy to say the kit bashing is so extreme and convoluted that they end up in Zeke's care as he is the only one that can make heads or tails of it. (Zeke would is combining Infernal, Divine, Arcane etc... magics and that is going to leave the TSAB a system or three behind... I'm sure their command structure would love to see taking up priesthood as legitimate field of study as iffy. Lack of Scienciness and all.)
This will allow them as inherited items for Zeke's family, use them as a cautionary tale and have them be around... use them for later stories et al.. You can temper it by having Zeke need to get part from TSAB.