The fremen jihad killed 61 billion people across the empire, including the sterilization of 90 whole planets, per details in Dune Messiah (quoting from a wiki, I don't have this kind of memory). It may be that life in the empire after this was over returned more or less to the same as what was there before, for those that survived - though I don't think the books go into any significant detail. Life on Dune was definitely better than it had been under the Harkonnens, but this is not necessarily true across the empire.
> Was not this the real moral of the story? Resist stagnant empire and explore the universe?
I think this is somewhat the general idea, but more specific. His main message is that charismatic leaders, even the ones with the best of intentions as Paul certainly was (and Leto II, though in a more complex way), are extremely dangerous and should not be trusted or followed. The empire overall would have been an unquestionably better place if Paul had been killed in the desert (except that perhaps the Bene Gesserit would have led people in an even worse direction if their plans had succeeded at the time). Arrakis itself would have been in a better shape if the fremen had risen up and overthrown their oppressors, but had otherwise stopped at that.