Some good suggestions. The cooked onions are delicious, and definitely worth keeping. I’ve used them in a roasted vegetable side dish, and within a veggie lasagna. The recipe is very well known though so there’s lots of suggestions online for what to do with them e.g. https://www.epicurious.com/expert-advice/what-to-do-with-onion-from-marcella-hazan-tomato-sauce-article.
Just to note, while black mold is common on onions and can be washed/cut off. The roots of some other molds can be highly toxic and discarding the visibly affected parts may not be enough, so be very careful.
Prometheus as a Christian allegory (spoilers)
I believe Ridley Scott has broadly acknowledged this theory, and, when viewed through that lens, the repeated symbolism throughout the film is unmistakeable.