Speach, CosmeticCorrection is fabulous for this. Run it after Calibration and before Alignment, or automatically with the BatchPreprocessing script. You must set up the template beforehand. I like to use Auto Detect for hot pixels, and also a master dark at an appropriate setting, and I also make detailed Defect Lists for bad columns. Hot pixels are nonlinear, and often escape the dark frame. CC will average in the values of surrounding pixels. Dithering is also critical when guiding! If they escape calibration, alignment drags the single pixel out to many. Good luck!