Yes, in the late game there really isn't any point in occupying or enslaving the population. Plus the best option then also gives you the best financial reward - hardly a difficult decision. If the financial rewards were reversed then this would help towards making this decision a little more challenging..

E.g.
Occupying:
High financial reward + difficult to control high population town.

OR

Exterminating:
Low financial reward + small, easy to control profitable town.