When I teach weather I start with the question "what is making the weather?", The question of "should I fly in rain ?" is really a subset of knowing what is the more general weather pattern. Leaving aside the issue of rain at temps near freezing, with respect to rain, especially steady rain, I want to know how and when the weather is going to deteriorate because it usually does when it rains. Then I want to factor in where I am going and how far. A bit of a miserable rainy day might be OK for a short flight over relatively flat terrain but constitute total unsuitable conditions if there are hills and valleys I have to negotiate.
If I have a choice, like showers from isolated towering Cu I will generally fly around the showers for a couple of reasons. One is most airplanes leak and other is it is usually bumpy under the Cu. I will never again fly through Virga as I had my airplane blasted by hail going through a patch of Virga that was light enough to see right through.....
With respect to SEP and icing, well that is easy. Stay out of conditions that can produce ice and if you do get any ice take immediate action to return to non icing conditions