Regarding the choices. The first one is bit of a how mercenary would think, why he should pay for something when you aren't getting paid anything?
That would be the interesting option >.> Second is the "heroic sacrifice" option. HentaiKami said it basically,
it's "safe option", nothing bad nor good come out of it as is, when you die (or killed) Atrix collects the soul and you end up as her servant... eventually anyway. Some other gods might not take it well, but that's their business. The last two are basically the same, it's the "murderous" way. It has other consequences one way or another.
As for the emperor. Here is the problem generally with rulers that have "absolute" power. When offended they can take a narrow view of things, there are several examples of that in the history. It isn't the first time ruler would order a family line the be killed. Hell that has happened regularly during wars versus other monarchs. Reading history books (and other historical records) isn't for faint hearted. Church records can be... enlightening about history as they collected a lot of information. I've read the 1700'ish local records, they wrote who had a STD, who was whose lover/mistress, and all kinds of tidbits and rumours into the them. And whatever local skirmishes happened is recorded in them as well.
And that being said. That's the thing being the developer, I can open doors that go both ways. And have choices that can either reinforce the decisions or negate some of them, to a point. Also, I know my fans (to a point), so I knew what reaction to the Ayaka's fathers would bring. There are fates written for him. Some can be satisfying conclusions, some not so much depending on the choices made. Will he get away with he did?
No, he will get what has been coming for a long time, but how the decision affects the MC and the empire depends on the choices. That being said regardless of the patch chosen there, it isn't "game over", that chain of decisions is just part chain, or a rope might be more appropriate metaphor. Just one thread isn't going to cut the rope, it isn't as strong but still functions. Can the situation be "saved" for most parts yes, might miss a character or two but it isn't a disaster based on single choice.
TL;DR: Nothing has been permanently fucked up, just need to wait until I get to the point where I can write and render them properly as there are things that take time to untangle... figuratively speaking. Of course unless several other choices are made that leads to that. I've never written an apocalyptic event happening during protagonist life before...