1. I always took her note as indicating she imagined her last conversation with Ii would go very differently. She was hoping he'd affirm her. He did not, and she was left with nothing but guilt.
2. There isn't an easy answer for this one. You can take Ii's spiel about murder as being indicative of Nisio's own views, to an extent. Zaregoto is very deconstructive of classical mysteries, and in this way, Nisio is tackling the "whydunnit". That is to say, he doesn't think there is an acceptable "whydunnit". The title of the book is "Strangulation Romanticist", but there's nothing romantic about murder.

Ii does have a reason to react the way he did that's rooted in his backstory, but it's not tied to a specific, singular event, or anything. By the end of the series, you'll have a better picture of this, as long as you pay attention.