I have not used cosmetic correction as it seems to reject good low signal pixels from my images
Why? Have you tried it in "defect list" mode? See the attached screenshot. Note that this is a quick test with your JPEG image - you should apply this process to each of your raw frames. You can do this very easily with the BatchPreprocessing script.
I am trying to get rid of it during the integration process using windsorized sigma clipping. The rejection map shows that it was rejected, however its still apparent in the stretched image.
That's strange. In general, a bad column is a well defined structure that can be rejected easily without uncertainty. If the low rejection map shows it as a set of parallel vertical lines (one line for each integrated image, since you are dithering), I don't understand why it hasn't been rejected. If the default "sigma low" value doesn't work, you should be able to get rid of these bad columns by simply lowering this parameter a bit. Or is this column defect more complex than a single column of abnormally dark pixels?
Anyway, the correct way to fix these defects is by applying CosmeticCorrection to each individual raw frame.