How do I negate a 要……了 structure?
As matter of fact, in my opinion, 不会下雨 is very good choice.

I tried to "directly" negate "要下雨了", but didn't find any way that is natural. The best I got is "不是要下雨了", which may be used to answer the question "是要下雨了吗？". It is simply a statement that "要下雨了" is not true, which may be "it won't rain", or "it is already raining heavily now", or something else.

Another way of saying it is "下不了雨", which means "it won't rain/it is not possible to rain".