I would probably say one of the last 2 options: "Fry the onions until they become golden brown" or "Fry the onions until they turn golden brown". The both mean the same thing and I would consider them the same level of "natural". There's nothing wrong with the first 2 options, they're just not my preference. Plus I don't think onions can turn red when you cook them, can they?

Fry the onions until they turn golden brown

I would say 3 or 4 but it depends on the recipe!

I agree with Shannon that I've never seen onions turn red from cooking. But "start to colour" is good too; it just means not quite as cooked as "golden brown".