Should there be a mod to switch this off in the future I will immediately do so. The Scandinavian countries are doing consistently well in polls regarding happiness of life, social and economic standards, etc. The US have the (or one of the?) largest world economies. There are countries much more cultural than where I live. There are countries more populous. You could say they are all winning, should we then start hating and fearing them? Ridiculous.
Personally, I think the domination victory should be the only one incurring this penalty. Cultural and science victories might be threatening but it's all about how they are used. I remember in Civ V that if I wanted to play peaceful, but I was miles ahead of the competition, I would help them out by offering research agreements benificial to them, giving them gold and resources, paying for their troops if they were at war. I did this because I wanted to play ruling the world like I would like to in real life.
This gameplay mechanism destroys that completely, and makes the game too one-sided in my opinion. Incidently, I played my first post-patch game (Nubia vs Congo duel) on Immortal, and I had a -134 penalty because I was winning. Because I got bored of their anger I took their capital in the renaissance era.
Edit: I just want to add that from a gameplay perspective this rule also does not make sense. If the AI considers "winning the game" all-important, how is getting angry with the soon-to-be victor going to help? Shouldn't they try to befriend and benifit? Send trade routes that get you more science, deal in culture to get your theming bonuses, ask for money, etc...