The main issue I had with warmongering penalties was that they were meaningless. Everybody hated you, but so what? They didn't actually do anything about it.
R&F improved that a bit with the alliance system, as warmongering penalties reduced your changes at alliance bonuses. But those bonuses are pretty meagre so still not a significant issue.
Since GS boosted alliances by tying diplomatic favor to them, I presume the game continues to evolve in a direction that creates additional challenges for warmongering - now measured with the new grievance system. But from reading GS player reports, it sounds to me like it has a way to go before the cost of bad relationships would approach the benefits of holding an extra city.