If they are going for realism, than yes getting any city from the enemy should create tons of unhappiness in the short run. It sucks for gameplay though. I think a minor solution would be to undo the production penalty from heavy unhappiness. Production or tons of gold is needed to get the happiness back up, so reducing it creates an "unhappiness trap." At the very least, the production penalty should not apply to happiness buildings.
The problem is not in local unhappiness which everybody would understand.
The problem is in the current design, where UNHAPPINESS is global, and happiness is local.
Ok, you have some wonders and resources which are still global, but the original concept nevertheless has been turned into a travesty.
Even having ALL resources will only give you 75 happiness, and most times you will just have less than all.
Wonders are not guaranteed from a certain level upwards, neither are the respective social policies.
Allowing the booty from a peace treaty to throw your victorious empire into turmoil just renders the whole "happiness" concept obsolete.
Edit: the very least would be your advisors popping up and warning you.