It's hard to tell from your scans, but it does appear that you could be bringing in detail that is really on the negative. Have you checked the neg under a loupe? Also, check the negative to see if you've got drying marks that went unnoticed before -- you might just need to clean that up.
If the sky detail is really on the negative, but you want a smoother look, one approach is to do a dual exposure. Burn in the sky just a bit with the original negative, then switch to a negative of a "blank" surface (smooth wall, etc.) for additional burn in with a bit of grain, but a reduction in unwanted detail.