Some thoughts:
1. What if all foodstuffs could rot, but only some could completely rot away? That is, all foodstuffs will eventually turn cursed at some point, but only the "perishable" foodstuffs will rot away completely. The time required for rotting would, of course, vary with the specific foodstuff. Large rations, for instance, might last a good 10000 turns before dropping one stage (B->U or U->C), while stomafillia might only last a good 200 turns. Only the things that already rot away would rot away, though. I also like the idea of the rotting rate being dependent on the background corruption rate, because the food is being corrupted. Locations with no background corruption would see non-perishable foodstuffs remain stable, while all foodstuffs would turn cursed almost instantaneously on the ChAoS pLaNe.
2. Herbs should have downsides. I mean, eating nothing but a herb designed to "fill your stomach" can't be good for ongoing health. Large rations give a lot of satiation, in exchange for being really heavy, and they're limited by how many you can buy in shops or find during adventuring... but Stomafillia just requires finding a nice herb patch and farming it to get a practically unlimited supply, it weighs nearly nothing and is worth much more in terms of satiation. It's also worth more as an offering, and has no impact on health. This seems rather unbalanced, to me.
One way to make them more balanced might be to have their effects made much weaker unless they are, say, prepared correctly. A common way to get real benefits from real herbs is to turn them into a tea - something based on this could work. Another way might be to have each herb negatively train a stat, or something.
3. If training above natural limits using sickness, starvation, rings of weakness, etc, were prevented in some way, the value of morgia and moss of mareilon would be somewhat diminished - there would only be so much value in collecting those herbs, because once you reach the natural limit in the three relevant stats, they become pretty much useless, rather than still being useful if used while sick, starving, etc. I believe there was a suggestion somewhere around here, for which I proposed that positive training and natural stat raises while a stat is reduced should be limited or even entirely prevented. I offered the idea, as I recall, that positive training effects should be reduced by 20% for each stat point of temporary reduction, so if a stat is "temporarily" reduced by 5 or more, you can no longer train it. Similarly, natural stat increases should be prevented if the stat is "temporarily" reduced by more than some number, for which 5 works well.
It makes sense, if you think about it - Toughness represents vitality, essentially... Sickness reduces vitality, which is why it drops Toughness most. Training Toughness while sick just doesn't make sense - you're low on vitality due to illness, you're not going to be improving it while in that state. So when Sickness lowers Toughness by 5, you can no longer train Toughness. You can still train Strength, for instance, but because you're weaker due to illness, the training won't be as effective.
4. Repeated offerings of the same item (except gold) should be nerfed - this would help reduce the value in collecting massive amounts of stomafillia. The same should also apply to selling large quantities of the same type of item to a shopkeeper - if they have 100 stomafillia in stock, why would they still pay top dollar for more of it? A side-effect of this is to reduce the value in continuing to let the Si duplicate for sac-fodder and to sell (I'm assuming that the casino exploits are addressed, so that money hasn't become trivial), which I think is reasonable. Something like, say, 1% reduction for each instance of the item, in terms of both piety and gold, would work - so, if you sell 100 stomafillia to Waldenbrook, and then try to sell another one, it'll be worth only 36% of the first one. For that first 100 of them, it would be worth just under 64x the value of selling the first one, assuming he had none in stock before you sold him any. The same scaling would apply to piety value of sacrificing them. If the piety value were to drop to the point of rounding to zero, the god could go "ENOUGH WITH THE <item>!", and no longer accept more of that specific item.