The Martha who pulled the trigger was a very near future version (cut under the eye - opposite side from what we saw when she was in the prime world, of course) was still very recent. She also had a larger cut under the other eye (we see the scar from that on Eve's face). I fully expected the two younger Marthas to get into a fight after Jonas was shot, but it looks like she gets it a little later.
So Eve thinks Adam is trying to destroy both worlds (and annihilate time) and Adam thinks Eve is trying to save her world by destroying his. I think. I just don't see how their actions are consistent with their goals.
Is killing Jonas the first concrete example of a deviation we have seen? Stranger Jonas is still around and his younger self had been killed (or has he?) I guess that could be another explanation - maybe Jonas is only mostly dead, and will develop amnesia, which would explain why Stranger Jonas doesn't remember.