A question about the game behaving in an unexpected way and how to fix it.

I got to LA. Pistol Pete told us about what's going on in Rodia. I go to Rodia. Watch the gatekeepers kill someone, then ask me for bullets to enter. I think "hey, it's fair, after all" and shot their stupid faces.

Then I got into a gun rampage around the village killing these jerks, meeting the locals, getting a shitload of cool loot and some new quests.

For some reason, I decide to free the major before getting on the quests I got. Then suddenly I wasn't able to cure the villagers, the lady who was with the farmer ex-husband has ran away (and I don't know if that could be a good ending for that quest) and the major's son will attack me on sight.

So, it looks like I have to ditch over one hour of gameplay and repeat the zone again to being able to not get some of the quests magically solved (and with a bad result), still, I don't really feel very talkative towards the leather jerks, and going around the city massacring them was really fun. Is there any way to solve this without the game fucking with me?