I have a problem with uncooked, sliced onion making me and other people feel uncomfortable in the stomach, sometimes whole night. However, when I eat tacos out in restaurants that never happens. Is it due to the variety of onion or do they prepare them in a certain way?
Adding salt and lemon should do it, or at least help a lot.
What you want to do is to chop them up and rub in a little salt and a splash of lemon juice (vinegar should work too). Obviously you don't want to add so much of either that you won't want to eat the onion. Leave to sit in the fridge overnight and enjoy.
Red onions are the best to use raw, and as I know a few people who get uncomfortable or upset stomachs when eating raw onion, even though others don't. I think it could be a particular allergy type thing. I'm not sure though so I will check that out. It could be good to store them in something though before serving (the onions not the people).