I think this is what is called a cheap twist.
I started watching Naruto relatively late. Growing up, I had friends who watched Naruto, and so, I grew accustomed to the characters, a bit at least. I never watched Naruto until a year ago, or so. And as an adult, I was overwhelmingly surprised by how subtle and how tight the Naruto story was. The animation, the music, the sound, the STORY. Almost everything was really good, when I was expecting it to be bad since it had ran for so long.
Getting to the point. The Naruto story is very subtle, and it is full of twists and turns, it is successful in using its own world and taking advantages of its own rules, making the series feel grounded and robust. The story is filled with symbolism and different ideologies, and surprisingly, most of the big things in Naruto are philosophies that have a physical represented form. For a "basic" fighting anime, it is a lot deeper than I expected, and it can certainly be appreciated on a deeper level. What I am trying to get at, is that your idea, is kind of cheap.
I understand what you want. You want a darker tone and a mysterious vibe to Naruto. I'd like to see that too. However, there are things to consider. Is KILLING the main characters off the way to do this? Now, the reason I called your way cheap, was because--YES. Killing off the main characters, would be a way to do this. Ask any stranger, what is the best way to make any series darker? Kill the main characters. It is a very short answer, and it is the first thing that comes to mind. This is why I called it cheap.
Naruto has been very successful in shaping the story without direct blunt force. The real question is; what is the best way to make the series grim? And this is a difficult question to answer, really. Because Naruto has grown more bubbly in the later seasons, becoming very much like Dragon ball because of the power creep. Boruto is very bubbly as well, it is very bright and has very saturated colors. This is a good sign, because they are likely going to create contrast very soon. What I mean is; If the previous episodes of Boruto are light and nice, and it suddenly changes to a darker theme, there is more impact. So either way, my point is, look forward to what'll happen, and hope it wont be as simple as this.