As you say, you might not even notice the difference between the two frames. The weight difference is quarter filled water bottle. So if you take that out of the equation you are really asking is the wheel upgrade worth $500? Carbon rims and caliper brakes are not known for the stellar braking ability so keep that in mind.
If it was me, I would go for the less expensive bike. No one that I know has ever said that they hated disk brakes after they tried them.