1-
A civil war was about to break out and with a civil war breaking out, the whole village could get weak allowing for other villages to attack. Basically they would be screwed.
So to Itachi it looked like either kill the Uchiha, or everyone dies.
He was also on a time limit and Danzo said that this way he could at least save his brother.
The Uchiha didn't back down, and Itachi choose to murder them so as to prevent the civil war, and also this way at least he could save his brother.
So from his standpoint the options would be:
Kill the Uchiha and save his brother.
Don't kill the Uchiha and either risk someone else doing it and killing his brother, or (if for example he confronts Danzo and manages to stop it) having civil war break out and everyone including his brother being caught up in it.
Danzo was just a person who gave the order.
He did admit that maybe it could have been fixed, and that he did the wrong thing later. But that's more or less what his perspective was at the time.
2- Obito couldn't return to Konoha before Rin died, because he barely could walk at the beginning and later on was stuck in Madara's place. Also from his standpoint, there was no need to hurry, he could train and get better then return.
He blamed the world for Rin's death, and when Madara proposed the Infinite Tsukuyomi plan, a plan in which everyone never had to suffer again in it. He agreed.
He came to Konoha because he wanted the nine tails. And also he blamed Minato for not being able to properly protect Rin.
Go to rain village and do what? It was war. And he killed all those soliders. His anger was more directed at Minato. Because to him it looked like he had failed and betrayed him. The person he trusted so much. It was a much more closer relationship and he felt heavily betrayed.
He was a heavily traumatized kid that went through a whole lot.
3-
What good would telling Naruto about his father do? Enemies could still be lurking all around, and they can target Naruto if he goes around telling people that he's Minato's son.
He didn't take the best care of Naruto, all the hokage's did various mistakes. The show kinda explores on the mistakes of them and what it caused.
Also everyone hated Naruto, Could Hiruzen trust another person to take care of Naruto?
I already explained Danzo's situation, also Danzo kinda gave that order in secret, so Hiruzen wasn't aware. And even if he was, to him, his options could be as limited as Itachi, either kill the Uchiha, or everyone dies (though he could perhaps do some other stuff, again, he wasn't exactly aware of that last order).
Also you make it look like these characters should be perfect and never make any mistakes. Them making various mistakes and stuff is kinda part of the anime. Human in real life make mistakes all the time too. Especially if they are heavily traumatized kids.