I have dealt with this on a few kitchens and every time it is cutting out the top of the molding so it fits the ceiling. There are certain styles of molding that this would be much easier to do or look better. It is the bottoms of the cabinets that need to line up not the gap between the top and ceiling.
The alternative is to buy crown molding that fits in the smallest gap. And then like bib said - add filler strips to the wider gaps. I do not think moving the cabinets is part of the equation.