what is the appropriate cook time for cumin before it turns into a smoky flavor?
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.