Someone is going to notice a huge radiated area in the middle of the desert. Not to mention, it is possible to detect such amounts of radiation.
Plus, these are moping-up operations. And dirtying up the place with fallout is not the best way to do it
While Deterrence is one of the main reasons why Nukes haven't been used often, there are other reasons. First, its really messy. Second, its needlessly destructive. There is such a thing as overkill, especially if one accidentally destroys the primary objective in the process.
Another thought: Maybe the Alaws don't have access to Nukes?
CB and Kataron knows about this, the information is not as contained as it should be.
Perhaps there's another reason why the Alaws are doing this. But what?