With the warmongering civs, it's just like others have said... get yourself a good stack of units who are ahead in tech or better trained, then go take one of their cities and raze a couple more.
This is what happened when I had Isabella. I actually had my scout spotting her units approaching and moved my stack of axemen I was preparing to intercept them, but the units she had were able to overtake a city of mine that had been just recently founded, then she razed it (I had two archers, she had two axemen and a chariot and sacrificed her chariot to weaken my defenders).
So I saw Toledo nearby and had the perfect plan for revenge. First, my axeman stack wiped out what was left of her units that survived, then intercepted the settler she sent to take the city site she wanted and took that out too. Then off to Toledo, which I easily took with my superstack of axemen with little losses on my side.
I also built two archers and a longbowman (discovered feudalism as I was building the second archer) and a new settler to reclaim my old city site.
I go after another city of Isabella's and she comes to me wanting peace and bribing me with 150 gold. I refuse her offer, go after her city anyway, take it easily (I had catapults now, so I used them to soften the defenses and the rest is history), and only after I razed it (it was too close to Madrid for me to justify keeping it) did I go to her and ask for peace, only asking for 180 gold as well, because I needed to take a breather from war... and yes, she did accept the peace offer.
And I've had Alexander in numerous games and have found he'll respect you if you are good to him in trade offers and you keep your military strong. Do both and he's highly unlikely to target you (at least in vanilla CIV, anyway).
Anyway, the moral of the story is this: Warmongers can be dealt with, you just have to play their game, only play it better and they'll eventually capitulate.