Considering enslaving and extermination immoral, I always occupy and never have had problems with population, except only once a loyalist uprising, but these things happen. Even on expert strategic difficulty. Maybee I'm just a great administrator :)
Also the choice depends on the style of play, somene, like me, tryies to be rather peaceful and play as I'd have rule being a real ... eee ... an omnipresent god of a nation :) Empathy.
On the other hand, some are just technologists of power trying to win the game quickly (like Alber Speer).