I am cooking a salsa that requires cumin in a large industrial kettle. It takes at least 2 hours to cook it down. When cooled off, it has a smoky flavor. So far, I don't want to use a substitution. I have thought about adding the cumin in for the last 30 minutes to see if it wouldn't cause the smoky flavor. Can someone tell me if there is an appropriate cook time for cumin before it turns smoky?
Cumin always has a earthy flavour, tending towards smoky especially if fried or toasted. So if you currently fry the cumin at the beginning you may get some benefit from not doing so and adding it to the salsa when you add the water-based liquids, but the chances are the best thing to do is omit it, or reduce it significantly. You may then get into experimenting with alternatives, but I suggest doing so in a scaled-down batch.
I went into a little more detail on flavour extraction and temperature in a recent answer.
I cook a lot of recipes that start with shallow frying cumin seeds. I find that the hotter the oil, the smokier/earthier the taste, whereas heating the oil less results in a milder cumin flavour in the dish.
I don't know if the same logic can necessarily be applied when using your industrial kettle, but maybe reducing the heat at which the cumin is cooked would give you the result you're after.