one way to reduce the contrast of polarised areas in sky is to do as follows (applies equally to PS and GIMP):

1. Using the freehand lasso tool, select the area(s) of highest contrast sky, including a reasonably wide margin. It is important that this margin extends somewhat into the non-polarised sky, and is of consistent width.
2. Feather the selection by a large amount - e.g. 120-250px (depending on resolution).
3. Using the Levels tool, adjust the mid-tones to the right (decrease contrast) by 5-20%; only as much as you think looks natural. You want to avoid creating a new light band at the edge of your feathered selection.
4. Invert the selection. The non-polarised section of sky is now selected.
5. Using the Levels tool again, move the mid-tones slider to the left this time (increase contrast) by 5-10%; again only as much as you can get away with without making the image look too 'shopped.

Done.

The overall effect here is to slightly lighten the dark polarised sky and slightly darken the rest of the sky, thereby reducing the polarising effect slightly. There is no doubt a more effective way to do this, but the above method is quick (10 seconds) and can often make the difference between rejecting and keeping a panorama.