I'll expand on my comments a bit and why I think these mechanics shouldn't have been ported over from the basic game.
I think you really have to look at the emancipation unhappiness penalty in civ4 from which the anger mechanics were derived. It creates a snowball effect as more and more civs adopt it, making the penalty for not complying prohibitive. As a historical representation of slave revolts and the worldwide abolition of slavery, it works very well. As a game mechanic, it reduces player choice and isn't fun. Clearly, it's the realism/flavour aspect that kept the mechanic in. So, we should ask whether the flavour makes a good fit with the changed setting in FFH.
From a medieval/fantasy perspective, most citizens are happy with the concept of monarchy. In a world dominated by religion and the struggle of good versus evil, I think most citizens would be likely to prefer a strong monarch. Indeed, in most fantasy literature where a bad monarch is overthrown, the heroes replace them with a good one, rather than abolishing the monarchy altogether. So I think republic unhappiness is really out of flavour for the setting.
Foreign Trade - The name of this civic doesn't really fit, because the default behaviour of cities is foreign trade with anyone with open borders anyway. If the regular civ4 name of 'Free Market' is considered out of context, something like 'Open Markets' or 'Free Trade' would fit better. Again, here, I don't see a convincing roleplaying reason for this to cause unhappy citizens. Consider the silly situation of having closed borders with everyone and the citizens getting worked up about whether they officially have foreign trade or not
WW - Removing WW from summons is a good call. I still think it would be a better game with WW removed or massively scaled back in the late game though. It's one of the few things that were badly designed in the base civ4 game. Persistent war weariness where you inherit the unhappiness penalties from a war that took place generations ago definitely should go; it's more likely after all in a medieval setting that the next generation would be brought up to learn 'these are our enemies, and one day we will have to fight them again.'