I'm going to take a wild guess and say it's the alternative idea that was mooted a while ago: make trees custom workshops. Then you just grow tree food and use that to make apples. I'd be interested to know how/if golden apple trees are implemented if that's the case, but I suppose some hefty apple-based research should do it.
Instead of making the petrification temporary, give it whatever tag is required to make it permanent. Then add a 1x1 field medical workshop that can be set up to process rare gems into cure mist that wafts around the workshop in a cloud and hopefully cures petrified creatures in the vicinity.
I was under the impression that the interactions weren't set up as curable, but if they can be, then cool. Another option is to allow golemising of stonies, so they can at least get up and about while the petrification wears off. Hmm, that'll need testing, see if the stone syndrome wearing off while the golem syndrome is active has any odd effects.
Speaking of cures, I'll having to look into giving some kind of syndrome immunity as bonus for drinks that include tonic water. Maybe by switching venom class for a while?
Yeah, could be that "lesser" cockatrices make one that wears off eventualy, and that "greater" ones ( ostrich/anaconda hybrids? 
) have a glare that stones ponies forever. As for where I am getting the idea for two differanting breeds of stonafing flightless birds, I will simply point to the idea from the dark reaches of this thread for things like Greater/Primal/ect Manticores and the like. Only fitting that there should be a differance in the run-of-the-mill one and the sort that sagas would be wrote about. A random, probably domesticatable wild one in savage biomes and a greater terror that can end a entire forts worth of defenders in a puff of sight are two different blends of emergancy.
Also, why have them turn into Alicorns? Would a !!Staggered Pony!! not do the trick, or somesuch? It seems to me if the pony is having his organs rearanged and sumsuch they should be rather.... disoriented.
If I did that, I'd probably make the greater whassnameatrice's permanent attack melee-only. We've seen how OP being able to shoot webbing is, permanent stoning at a distance as a standard attack is far, far too much. Really, if it lasts a month or two, it'll cripple the fort anyway. Oh, and unless some diomedians come along with silver whips, everyone being turned to stone would just leave the fort in stasis, not properly ended, and with an annoying little creature nibbling on stone statues.
