You've skipped through it so you should already know that in the next update Nodoka is back. Things get reset when resets happen, which is why shit can go down at reset time. We've seen Makoto try to kill herself, we've seen tons of Maya being hanged and crucified during happy events. Even Ami was basically crucified and flayed during the CH3 reset, and there's a chance that's why her personality's different.
So is your problem seeing murder? Seeing dead bodies? or the lasting death of a character? The last one hasn't happened yet, and realistically cannot happen. It's also what you asked about in my opinion.
Even if the dark route changes the rules of engagement and characters dying during that time stay dead (Like I imagine Makoto would be the first to try to kill herself in front of the others to prove you can't die, except it just happens this time, maybe a moment of her realising her mistake before she bleeds out), the mechanisms to bring them back after they do what they need to do during dark route exists. They can just reset people back to life.
The closest thing to a lasting death in the game is Maya's reset but even the game at this point has given lots of little hints that she's probably not entirely lost. And with the other points that the game is building up to with her, Prime is probably coming back before the ending of the game (like I wouldn't be surprised if CH4's ending is Maya Prime's return, the game still needs time to expand upon the history they shared when Maya was being tutored, and explaining why there's a ton of hints pointing at the fact Maya might not be real. Her purity routes / true ending being used to explain all of that would be a shit time I think.)
In the end, kinda yeah, for both questions. This VN can actually make you feel things other than horny or angry, and that's a serious achievement.
Like that Maya scene that never really got you. It's because you didn't notice Maya coming out of her shell before it, that entire chain is her wanting to spend time with the person she loves while being afraid of the fact that if she says she loves him he's gonna be deleted again. It already took her thousands of years to find him, even if she was prepared to do it again.
The next update is the christmas chain, and that ends with the two finally talking to each other, and even that brings up the happy moments they've shared which shows the fireworks and her eating the melon during the festival. There's even a convoluted theory that during 0.47 we get a moment of Prime saying "I love you" to Sensei. I imagine you didn't see Io's events either since I believe that's hidden behind Sana's invites and you probably gave up after the text skips stopped showing events.
Of course if we have to signal upcoming trauma in 0.47, Chika gets tricked into an orgy for 10 years or something with the Great Pareidolia Mall's denizens. Jury's still out on whether it was a physical event or just mental trauma and that's after her eating Rin out after Rin committed to moving on from Chika so she can't decide whether she's happy about it (and if you know about consent, it has to be enthusiastic)
0.46 just has a moment of emasculation for Sensei. Kirin is the one who gets traumatized if anything. Imani gets disrespected.