Kyuubey's goal is explicitly long term (and by long term I mean heat-death-of-the-universe long term). If his actual plans are for immediate, short-term gain, then there's some serious cognitive dissonance going on.
The problem is that the risks that Kyuubey takes appear to have worse payouts over the long term. If you can have a more witchouts over a short period (even a single witch as big as Kriemhild Gretchen), but this results in fewer witchouts in the long term (i.e. over the thousands or tens of thousands of years that humanity could be expected to exist), then this is a worse strategy. Maybe we're wrong about Kyuubey's goals and he really is only interested in a short-term payoff. Or maybe we're wrong about what his plans are or the magnitude of the benefits and what appears to be short-term greed really turns out to be more profitable in the long term. But something is wrong either with Kyuubey's plans or with our perception of them.
Also, it seems to me that any Standard Operating Procedure which allows ones' enemies to make unrestricted wishes is intrinsically flawed. There has something here that we aren't seeing. Maybe Kyuubey has been playing things completely off the cuff and he's terrible at improvising. Maybe he's insane. Or maybe his goals and plans are not what we think they are.
If normal human meguca are regularly cleansed from grief, they would be kept safe from starvation, but most teenage girls would hit some sort of emotional breaking point within a few years. For regular humans, this just means that they would be depressed for a bit and then recover, but for a meguca it would mean witching out. The proportion of meguca to witches at any given time would make the witches an anomaly, but witching out would still be a near certainty for most girls.
The question here was whether or not Kyuubey would be motivated to sabotage a clear grief seed cleansing operation. There's not enough evidence to be sure, but it's possible that it would be worth it for him to help the operation (or that we could at least convince him to leave it alone). Obviously, we want to cleanse people regardless of Kyuubey's wishes, but it would be easier to do so (and we would be able to save more meguca) if he's not actively opposing us.
Witch outs are not generally assured at all under those circumstances. The first thing to understand, is that witching out is responsible for 90-99% of the grief created by a magical girl over their lifetime. Under normal circumstances (i.e. no sabrina), Kyubey may well have the most efficient system.
Imagine a society of meguca 5-10 years down the line with free access to clear seeds. What social codes would grow in a society of (possibly immortal) mages which no longer has any reason to fight? For starters, there would be a lot more meguca, most would have meguca friends and meguca allies. It would be considered the neighbourly thing to do, to hold a friends gem during times of distress and keep a seed pressed to it. With such a small risk of hatching, people would keep their gems in transparent, padded cases with the clear seed constantly in contact, so that no matter how they fuck up they wouldn't spiral. Witch outs would very much be the exception, not the rule, under these circumstances.
It's likely that more girls would die from gem destruction than from witch outs... Which would actually be a problem for the growing population. At 10 years down the line there would be more magical girls that grief seeds, so a system of sharing would have to emerge... at 20 years there would be closer to 40,000-200,000 meguca worldwide and a severe seed shortage shortage. An average city would have 60-300 meguca with only 10-30 seeds. At this point you might get two or more girls grief spiraling at once, with only one seed between them. Because lots of girls are friends a spiral of one could spread to others, leading to the dwarf fortress tantrum spiral, except it leaves a city with 1/4-3/4 of its meguca witched out. While a tragedy, this would form a self-regulating feedback loop which would slowly increase the number of seeds in circulation, keeping the ratio at just about the level required to cause quiet desperation. At 25 years this strategy become untenable as large groups of meguca fight over scarce clear seeds and gem destruction rises.
The problem of long term seed shortage could be avoided via familiar farming, but that just puts the life of one magical girl as more important than 10 normal humans. I would still expect it to happen in a lot of groups, however. With magic use no longer limited, meguca could theoretically do enough good that familiar farming would be the moral thing to do. A rule that a meguca must save 20-50+ lives through magical healing or otherwise before they're allowed to own a clear seed (while still getting cleanses from a communal seed) could be implemented. In this manner the meguca population would be a net gain for humanity. Familiars could be farmed mainly in war zones, on death row, or in places with a very high average age in order to reduce the number of life-years taken to produce each seed.
The Meguca population has no real limit. Sabrina can cleanse a theoretically infinite number of clear seeds every year, given use of time stop and other magical fuckery. She could even live a normal life at the same time, because of her impressive multitasking skills. There is population growth, but no predation. With magical healing, meguca durability and proper soul gem defensive casing there should be functional immortality. Once the population reaches 20-100 times current level (depending on the exact amount of grief created over a year and by a witchout), Kyubey would be receiving more grief from the planet than before even if witchouts are kept to zero. Even if the population of meguca becomes greater than the population of normal humans, its growth is restricted to the number of girls with potential that appear each year and each meguca only needs a clear seed once, so familiar farming would not impact the human population on a macro scale.
Kyubey should accept such a proposal. He is greedy, and thinks long term. They've been doing this for thousands of years. The chance to get more than 10x the grief each year from a world is not something I think he is likely to pass up.
As an aside the possibility of familiar farming raises interesting ethical questions about meguca revival from seed form. If a witch is turned back into a magical girl, but it still has a familiar out there, and the familiar becomes a witch, and that witch is also revived, what happens? Do you get a clone of the magical girl? If one girl saved is good, is two better? Can the clones use magic? Does that imply we're also cloning the soul? A healing based meguca with a clear seed could save hundreds or thousands of lives, does it then become ethical to sacrifice 2000 humans to create 100 meguca and 100 seeds which will then save 10,000-100,000 humans? I lean towards yes, since if we know that a girl has saved 500 lives, then we know her clones will also likely save 500 lives. More people living is better than less people living, and 20 is less than 500.
TL: DR Kyubey should accept a grief trade proposal if we put it in the right words.
