The problem of red noise in blue skies is fundamental to Bayer sensors (which effectively means anything other than Sigma DSLRs). Each individual sensor site is particularly sensitive to one primary color, and the camera uses a "demosaicing" process to detemine the color for each output pixel.
In a blue sky, the sensor sites dedicated to Red aren't picking up much of anything and are mainly just producing noise. With most camera sensors, the Red sites need to be amplified quite a bit to achieve proper white balance in daylight conditions. The result is red noise in the blue sky.
What to do about it? Here are some options.
- Nothing. People get all worked up about noise that isn't visible in the prints. You'll always see noise if you're pixel-peeping at 100%.
- Use a lower ISO. ISO 800 is going to be noisy on anything less than a "full frame" camera. Take off your polarizer and use ISO 200.
- Be careful not to overexpose. If you overexpose the sky it will overload the blue channel, giving the green and red channels more power there, and the red channel is mostly noise in a blue sky. If you properly expose, the sky will be nice and blue without needing the polarizer.
- Use a good noise-reduction tool, select the blue sky, and reduce the noise in the sky. Go easy on this. You'll never remove all of the noise. You just want to remove enough noise to get good prints (or whatever your output medium is).