Unfortunately, there's no way to chemically counteract the fumes - it's actually the oil particles suspended in air that are irritating your eyes/throat. You really have to vent the area. Coating the peppers in a bit more oil when you're cooking them can prevent some of the spice oil from volatilizing, but you still will need to vent.
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For starters, better ventilation couldn't hurt. Try browning the hot peppers in the oven so you don't have to remain in the room with them during cooking.