Yes David, adjusting to a non-state religion's appearance in your cities can lead to 'interesting times.' That's a factor of Hephmod being closer to a simulation (i.e., is more realistic) than the regular game. There ARE ways to minimize such unrest, such as putting a priority on happiness issues in such cities.
With Free Religion, each religion's unhappiness is balanced with it's temple's happiness. Also, each religion (even without buildings) gives gold, science and/or culture.
If you have a civil war, know that you can still prevail (and it can be quite EXCITING to boot)! With a little luck, that neighboring civ that is such a threat will have its own turmoil in its own good time.
There are NO issues!
Only features* we have to take time to adjust to. 
* As I will have to do to adjust to the 3.19 rendition.
n.b., I'm still with the pre-3.19 version, and play at Noble/Prince difficulty (huge/marathon).
With Free Religion, each religion's unhappiness is balanced with it's temple's happiness. Also, each religion (even without buildings) gives gold, science and/or culture.
If you have a civil war, know that you can still prevail (and it can be quite EXCITING to boot)! With a little luck, that neighboring civ that is such a threat will have its own turmoil in its own good time.
There are NO issues!
Only features* we have to take time to adjust to. 
* As I will have to do to adjust to the 3.19 rendition.
n.b., I'm still with the pre-3.19 version, and play at Noble/Prince difficulty (huge/marathon).


. All the civics are based on this core idea that there is a trade-off. Slavery increases productive improvements and gives you the hurry production ability, but the trade-off is general unhappiness; similarly, free speech gives you a huge cultural boost but the trade-off is that people will be vocal about dissent, increasing war weariness and giving unhappiness for jails. If you look at all the civics, you'll see the whole system is based on this idea.
Right now it's set at "-2" (two unhappy faces per non-state religion); in vanilla it is set to "0."
In fact, one of the things the mod tries to do is move away from the triumphalist Western master narrative of progress through capitalism. Free market societies now have to deal with additional unhealthiness from letting companies pollute and overlong working hours for laborers. The labor unions civic, for example, is a simple trade-off: do you want your workers to be healthier and happier, or more productive? If you want to be a real despot, people will resist you, and if you are "too" liberal, you will have to deal with the fact that what makes people happy isn't always what's good for YOU.