So I am an hour or so in - basically made it through all the cutscenes and tutorial and got to my cave and began exploring and I saw a gold marker for a "rescue the wenja" quest. I sneak up and start killing the guys and they kill the wenja. Is this story breaking? Do I lose out forever on 100% completion? Am I screwed now for an upgrade that could only have been gotten from that mission? I have no idea how important this mission was that I just completely ruined. I am early enough in the game I can just quit and start over again but let me know if that is what I should do. Thanks!
These gold-labelled wenja events are optional and an opportunity to acquire new people for your village. If you miss such an event, no worries, there are plenty others coming up all the time in the game world. There are other types of events as well, red-labelled, which are more kind of mini-quests (you normally have a quest giver and the actual mini-quest is added to your map-menu).
Use the filter option in the map menu to see which is important for the story and what isn't. In the end Farcry Primal is both, a game which offers a lot of freedom, but then again the story unfolds in a certain way - it isn't really linear, but it unfolds in a linear fashion in the long run nevertheless. Just enjoy yourself and get used to live in the wilderness. The game plays as well very different dependent on the difficulty setting - just an example, if you choose easy, rivers have pretty much no crocodiles in them, or when you choose survivor mode, you will never have more than 3 health bars.
The main thing in the game is to really become Takkar, the well known beast master, and attract people to your village by helping them out and in the end conquer the land of Oros for your fellow wenja people. Taming beasts is a major aspect of the game and quite enjoyable. So, don't give up, just go with the flow and become Takkar, the beast master, the one who'll make the world livable for wenja again.
I found that normal mode can be quite chaotic at times - the higher density of wildlife and people in the game world leads to emergent effects, which are raised by complex interaction between animals and/or humans. I find it a lot more immersive in survivor mode, lower density of animals during daytime means less opportunity to hunt, but as well having to deal with a lot less chaos - at night time though it is the other way round - more chaos in survivor mode - well, you will experience it yourself - but keep this in mind - you can have quite different experiences dependent on mode and difficulty setting.