Warmonger penalties just don't factor in my game-play.
I've had friendly AIs surprise DOW on me, I just figure that making an effort to keep good relationships with the the AIs isn't worth the opportunity cost of not expanding in their territory to get what I need.
Also, if any AI declares war on me at any time during the game, I activate my righteous vengeance streak, which means that they're fair game to me for the rest of the game. So having a double or triple negative warmonger score doesn't really change anything.
I usually play King level, and try to alternate between Science, Cultural and Domination victories. Playing for a religious victory doesn't seem very interesting to me and never bother with it.
Those friendly AIs, any chance that was mostly in the Ancient and sometimes in the Classical era? The later the game goes, the more reason an AI needs to declare war.
Also, sounds to me like you're calling the "all AI hate me" over yourself. The game is built in such a way that early wars happen very often, which means that you'll have one or more most likely every game. If they're then "fair game" to you for the rest of the game, and you attack them 3000 years later, then everyone else is going to hate you for starting a war, of course. If you want to conquer stuff without everyone hating you, do it early, do it fast. Later in the game, do not take more than one, maybe two cities. Take one more than you intend to and then give that last one back in the peace deal, and the AI you conquered the city from won't even hate you.
In my current game (now Industrial Era) I've played this way. Early on, I got declared a joint war by Persia and India. Being Australia, I turned it around, conquered all of Persia and made peace with India. Slightly delayed my first Classical Era tech to not get any warmonger penalties for this. Then playing an expansive but peaceful game, having two civilizations worth of land to expand (mine and Persia). In the medieval era, Russia declared war on me with a surprise horsemen rush. I fought it off, went on the offensive, took his two cities bordering my lands, then took St Petersburg, let him cede the two cities on my border, gave him St Petersburg back. Total warmonger penalty: 15, gone 30 turns later, as this is how warmonger penalties work. I got 3 denouncements during this time, right now there's 1 or 2 still standing (I've barely played beyond when the warmonger penalty was gone), of the, I think 9 civs I know, there's 2 denounced, maybe 4 unfriendly and 3 neutral. That's while all the relations are still bad because of the warmonger. I expect to have some friendly faces within some 30-40 turns.