So, I'm trying to deal wigh God's Militia, and by deal I mean I want to break their spirit, make them doubt their faith and make them decent people :)
Here come some bugs (I guess).

1. Free church slaves
Maggie asked me to free people held in the church. I simply can't do this: eliminating every knight \ paladin \ priest in the yard does nothing, they still don't follow me.

2. Double Louis
Yeah, there are two Louises now. One is in the slave pen and the other in Pilgrim's Inn. One in the pen says he can't leave before I free the other slaves, one in the inn ended quest given by his brother (but Maggie still refuses to aknowledge slaves are free)

3. Broken Man is missing
First I asked everybody around (both the church and the village). Then I tried again and typed 'Veronica' manually in their dialog boxes. No dice. I'm afraid to continue with the main Church questline because I don't want to kill that poor guy by accident :)
EDIT. All right, I know who the Broken Man is. That's good. Clever clue :) But I can't confront him about it - the only dialog option I have is about joining his chapter of the church. Typing 'veronica' still doesn't do anything.
Helping him gain control over the church makes talking to him impossible (he only thanks me in a dialog box).

4. Mathias and Rodia
I solved Rodia lawfuly (Mayor back in his office, trade route with Angel's Oracle established, son's quest taken but ignored). Yet Mathias was happy that I killed people who resisted him in Rodia and asked me to 'do the same' with Angel's Oracle.

Yeah there are quite a few broken quests in California atm unfortunately, especially the ones linked to God's Militia if you want to do it relatively peacefully. The beta only included Arizona, so California was only tested in-house by the devs, which apparently wasn't nearly good enough.

Personally I just chose to kill the Militia, because people who would execute someone because he ate shellfish really deserve to die, but I think to disband them in a peaceful way you need to reveal the fact they're behind the drug dealing.

Broken man is a nice fella once you make him friendly. There is a good chance he'll reform the Militia in a good way :)

Another major bug related to this quest :)
After restarting, ignoring Heidi, ignoring everything else and going straight to Veronica the quest triggered properly. Unfortunately early on I... well, offed Jones :)
Now, many stages later, Jones is supposed to take over the Militia and I'm send to eliminate him... but he's already dead. Questlog tells me to go to the Observatory and witness signing the peace treaty, Ascension stands on the street and urges me to eliminate Jones, nobody's there to sign the treaty and I'm stuck again :)
Also, Maggie and Louis are gone (after I secured slaves' release during Council meeting) so I can't get my reward end their quests (maybe the game thinks there is some big battle between Rangers and Jones' militia, that's why they're not there).
Another try tomorrow :)

And another game breaking problem - i managed to kill Fealty Mayweather but he doesn't have a key for gate to radio tower. Apparently he didn't drop any loot at all. I'm stuck :((

Wasn't Fealty the wife (with pretty masculine avatar :))? Tell her you want to join, she'll call her husband.
Or bruteforce \ lockpick the gate :)

Everyone in bastion is dead. Brute force/locpick unappliable. Grenades and launchers also ineffective.

So, after following the quest as it was meant to be followed (no 'unfortunate accident' happened to Jones this time) I secured peace between Hollywood and Bastion. Louis appeared in Pilgrim's Stop and concluded the quest properly, but Maggie is missing and the rest of the slaves remains in the pen. Well, I guess I'll have to skip this one...

One more bug unrelated to this quest:
Ending slides for Railroad Normand Camp shows that Topekans won but can't run the trains. Fine... but I secured peace in the camp... Can it have something to do with one of Camp's representatives dying during the final assault?

Probably they miss train detail, break swing in Atkinson's camp.