I'll defend to the death the right to digitally remove dust from a scan.
As for the rest, in the past I've used the phrase "you should only do the things with a scan that you have to do when you print in the darkroom". By that, I mean choose an appropriate crop, good exposure, useful contrast and, for colour, colour balance. You should also avoid the extremes that are available only in the digital world, if possible.
Dodging and burning is definitely on the edge, but I'll confess I've darkened a sky or two in my time.