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It should be OK; we haven't heard about any cautions regarding hornworms affecting edibility of crops in that respect. After harvesting, cut out any damaged areas and throw out any rotten leaves. Then wash the greens thoroughly just before eating, using cool running tap water. You can blot the leaves dry with a paper towel or use a salad spinner. Be sure that your hands and any utensils/tools and food preparation surfaces are clean. (It is recommended that hands are washed for at least 20 seconds with soap and warm water before handling food.)
Are these cocoons on a caterpillar? See the photo of the tomato hornworm with the braconid wasp cocoons above - these are one insect per cocoon. Braconid wasps are parasites of the hornworm. If you see these on a worm, leave them be. The hatching wasp larvae will take care of the hornworm pest.
The eggs of a cabbage looper are laid with no protective covering on leaves, singly or in small clusters, and are whitish yellow to green. Each pupa is encased in a thin white cocoon under foliage; the pupa itself is green, then turns brown to black, before transforming to a moth. A few insects make egg cases, such as praying mantids and spiders (egg sacs), which contain many eggs. A common tomato pest that might do this, though, does not come to mind at the moment.
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The pest you're describing sounds like the tomato fruitworm, which is known to bore into tomatoes and cause them to rot. Once they get inside the tomato, there's not much you can do, so stop them beforehand by routinely checking for eggs on leaves and spraying with a natural insecticide, like Bt (Bacillus thuringiensis).