Hmm... That's tricky. Was the decision to go with 2 different crown moldings intentional? It looks a bit odd when that's all you're looking at, but I can understand the contractor's dilemma as you can't have 2 different crown moldings meet up. Maybe it's the kind of thing you won't notice if you're not looking for it. I know there were lots of things I thought would bother me while our house was under construction that faded into the background once we started living in the space.

If you're pretty sure it will continue to bother you after the spaces are finished, you could have your contractor add a stub "wall" between the rooms from the ceiling that's low enough to allow for crown molding. Looks like you have a very pretty kitchen.

To give you a visual of what I'm talking about (not sure if "stub wall" is the right term when it's coming from the ceiling), here's the opening between our kitchen and living room areas. We don't have crown molding, but chose to trim the opening out to make it easier to transition between wall colors. You already have stub walls defining the space on either side, so in your case it would just involve adding a bit of wall at the top of the opening and adding your crown molding across the whole ceiling area.