I thought DSLRs in general subtract a dark frame above a given exposure time?
Not sure if subtracting another one would help but I have to admit I never tried it.
Some suggestions on noise reduction from my own (rather beginner's) experience:
From a second point of view (not the photographer's), noise is often less of a problem than the artifacts you get from noise reduction/ the lost detail. If detail is first blurred and then, in part, recovered via sharpening, this may look better onscreen but make a worse print than one with a tad of noise.
You may want to try to mask the sky, convert the image to LAB and work on the single channels. On the chroma channels, try the "dust and scratches" filter. On the luma channel, use the (selective) blur tool here and there.
I have tried Neatimage but did not like it. In general I now stay away from either sharpening or blurring (i.e. noise red) of the whole picture (as long as its properly focused) and rather do it selectively. Of course its another thing when it comes to uprezzing/downsizing pics for which it may be still handy but I have only now started looking at that and cannot tell much about it.
I would think you'd roll better with keeping the ISO at its initial value and increase the exposure time to compensate for the lost stops.