"Well... talk about your big reset button ending - that didn't make sense. I KNEW the skience would bug me this week. Blowing up a portion of the atmosphere would lead to dead planet, not just clearing the gas. Also the chain reaction for igniting the whole atmosphere happened rather fast yes?"

I kind of assumed that it was a special machine he created... because he didn't just send up any old thingamajig that could ignite the gas, he sent up an "atmospheric converter" which in some magical Gallifreyan-ey science way probably only burns up the clone feed gas.