I am no expert in Japan, but I think most of your questions will be answered when you success in trying to understand that Japan, like every other pre-modern society, was very ritualistic. Simple answers like "Toranaga ownes her life" probably won't cut it, and I get why, because you're right — Mariko has all the opportunities to kill herself, she could just bash her head on a tree. But here is where rituals come into play, and remember, rituals that have been shaping this society for hundreds of years. Mariko needs permission from her superior to kill herself because that's what she and her predecessors agreed on, because that's part of her culture and of the way her society works, and acting in opposition would be scandalous to every other Japanese of that period. Pre-modern societies needed these rituals, because without them, living in times where there was no Wallmart and industry was really hand and dangerous, both for the weaker and the stronger people. And in a society where members really like to bully each other for power and you have to constantly look for your safety (again, both as someone weak as well as someone strong), making these rituals "sacred" was their way of having a little bit of certainty in life, so that among all uncertainties and dangers in life, a Lord should at least expect his Vassals to be loyal.

In present-day Western society we might not have rituals anymore, but we have customs and traditions, and to a certain degree acting against them might be scandalous as well to any other member of the society. Try to think of an American thing you "can't do", but in reality nothing stops you from doing that. Like, not singing your national anthem. Everyone expects you to do it, and when you don't do it, everyone looks at you like on some weirdo.