After just two days of light use at home my red smart cover had a couple of small dark splotches. I have no idea what they were. Anyway, I rubbed it down with several applications of Lemon Pledge (furniture polish). This removed the stains. After it dried the leather has a semi-gloss finish and is just a bit darker. The way the leather soaked up multiple coats of Pledge leads me to believe that the leather wasn't treated with anything.
I am concerned that the microfibre (<- Canadian spelling, BTW) of the cover will pick up particles when it is folded behind the iPad on a flat surface. I will clean it often (with a lint roller) but mostly I just won't set it down with the microfibre out. I have been folding the cover into a triangle with the leather out (opposite from Apple's videos) and that works well. When I set the iPad down flat, I will either remove the Smart Cover or leave it open like a book.