He had the one device, but I don't think he had the plans or materials to mass produce the device, thanks to the sacrifices made by the Regula I crew. And if had detonated the device to rid himself of Kirk, then he wouldn't have been able to "reverse engineer" the only device he had at his disposal to try and mass produce from there.
If he defeated Kirk without using the Genesis device, then he could try to reverse engineer it (and he is a quick study), seek out the means to mass produce it, and then he would be a terror for the whole galaxy to reckon with. He could basically destroy a planet's population because the Genesis device reconfigures the target world "in favor of its new matrix" (as Spock pointed out). The Klingons saw this too. An ultimate weapon that could wipe out the indigenous population (be they native or colonial) and make the world suitable for whatever life the user chose to implant on that world.
Granted, Klingons and humans could conceivably live on the same planet, but conditions for one race might not be very comfortable for the other. The Genesis device can be programmed to replicate the conditions for the race that intended to use it.
Or, in Khan's case, that which he could not conquer, he could destroy, without forethought of "environmental conditions". Or, he could even program the Genesis device to be a true weapon of destruction, and render the target world uninhabitable, perhaps irreparably so.