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!


* 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).