An excellent question! This took some time to research, but you sparked a curiosity as I have four cherry trees and a large apricot tree in my yard and compost all seeds and pits. Here is what I found:

According to Anne Anderson, a Professor in molecular basis of plant-microbe interactions in the department of biology, “many microbes will degrade cyanide-- it’s a valuable source of nitrogen-   so that in the normal composting process the cyanide will be degraded. In other words, there would be no problem with cyanide uptake into plants. Exception could be if the pits were pooled outside of the compost pit and vinegar added (vinegar sometimes is used to defeat weeds) then the release of cyanide could be a limited time problem. The apple pips are so small that they are not a problem. The apricot hull though is so difficult to compost it takes years as it is lignified cellulose   so it may not be the best thing to make all of your compost from!  My squirrels seem to love to move them all over the garden.”

The literature I found on this topic was conflicting. A study published in the International Society for Horticultural Science found that amygdalin (cyanide found in apricots) played a role in the replant disease of peach and nectarine. The authors recommend future research focusing on the nature of amygdalin, or perhaps more specifically “cyanide”, its accumulation and breakdown in orchard soils, and the interaction with other soil associated stress factors (e.g., nematodes, nutrient deficiency, fungi, etc.) that might also be affecting tree growth and survival. They conclude their article by stating “If amygdalin-linked toxic substances are indeed a key causal factor of replant disease, then management strategies that minimize the release or accumulation of amygdalin in the orchard soil should lead to reduce or prevent the problem.” (Sotomayor, Gonzalez & Castro, 2006).

On the other hand, an article in the South African Journal of Natural Medicine, Issue 22: 14-17, states: “We mistakenly believe that the pips of apples and the inside kernel of apricots, peaches and other stoned fruit are  ‘poisonous’, because they contain ‘cyanide’. However, cyanide, as it appears in its natural organic form in a molecular complex in food in the form of nitrosile, is actually vital to our health. Nitrosile or vitamin B17, as it is also known, occurs naturally in seeds of apricots, peaches, apples, prunes, plums, cherries, nectarines and cereal such as millet and buckwheat. Macadamia nuts, mung beans, butter beans and certain strains of garden peas all contain this essential nutrient. The nitrosile compound containing the cyanide has the ability to destroy cancer cells, without doing any harm to healthy cells. Cyanide also occurs naturally in vitamin B12, which is not seen as a ‘deadly agent’, but rather a vitamin vital to our health (vitamin B12 is known as cyanocobalamin).” (Preez, 2006).

It seems the thinking leans toward acceptability of composting apricots and other stone front as cyanide is degraded in the decomposition process.