Nice photo!
As far as the smudges go...there's not much you can do. The sky is fixable, taking into photoshop, make a selection, then doing a gaussian blur would probably remedy that. I think I see some smudging in the roadway and trees (not sure cause the pic is kinda small) but sadly there's really nothing you can do when the smudging is over a detailed area of the image like that.
Yeah. I too mainly use Aperture (Program) too and it does have a clone feature.
To the OP, just use the retouch tool and then the box will come up and change it to clone.