Yeah, I agree. Severe diplomatic penalties should be the result, as well as permanent Happiness penalties (if under Freedom). The only problem is, where would that leave all those trigger-happy warmongerers who don't feel like taking on a new cities every time they go off marching?
Perhaps there's nothing wrong with that. The Civ series has always had a fairly relaxed depiction of razing cities, but perhaps that should be changed so that it is a Really Big Deal. Wanna stomp on an enemy's face? Fine, but leave the civvies out of it and don't go destroying entire cities. But this would also alter the impact of settling far-flung colony cities and the like; that would also become a Really Big Deal, as you would no longer be able to just flick away (with relative impunity) that pesky little 1-pop city settled by Hiawatha from across the entire world.
Or maybe preservation of the current balance is the best thing, in which case an alternative option would have to be added. Perhaps you could choose to de-militarize the city, leaving it under the owner's control but disabling the ability to station a military unit there and disabling the city's ability to fire on enemies. Or perhaps the conquering/freeing could result in a shrinking of its cultural spread and a moratorium on re-spreading, if your beef with the city is territorial. In both cases, re-militarization and/or re-spread options could be included as part of the peace negotiations.
I dunno, just thinking aloud. It'd also be fun to have a "Create City-state" option, with the freed city becoming its own little side, minus the various political and other bonuses of true city-states.