It's honestly still quite unclear A: what your render settings are (if you are using defer atmo or not, and what your AA setting is if so), and B: whether the rays are in just atmo, or cloud as well (I assume the latter based on your description).
In general when you have a very bright area against a very dark one, as in the case of rays against a heavily shadowed background, you are going to get noise without higher sampling levels. If you are using Defer Atmo I you might try increasing AA first, rather than adjusting atmo or cloud quality/sample levels. Though it might be good to determine what the main source of your noise is, whether clouds or atmo. You could do this by adjusting the quality/samples of only one of those at a time and doing crop test renders. If the noise changes when you increase or decrease quality of, say, atmosphere, then you can assume that atmosphere plays some visible role in the noise. It doesn't necessarily mean it is solely responsible for it, but eliminating noise from cloud or atmo is a good first step, then you can adjust the other element(s) to remove the remaining noise.