You've always needed to select your route on Day 5 and the scene in question happens on Day 7, so not entirely certain how you wouldn't have known what route you were on. Since that scene released, we've made it more obvious what is going to happen though the outcome is still the same if you do it on Diego's route.
The intention with that scene was to have an outcome which you couldn't necessarily predict and for Diego's response to it to be particularly flawed and human. The protagonist hasn't strictly done anything wrong, and from that perspective the outcome seems entirely unfair. At the same time however, it isn't wrong for Diego to feel how he does and his reaction is something entirely human. It isn't a black or white situation, rather one that is messy and complicated just like real life. It was an attempt to experiment with shades of grey in our storytelling, though in hindsight, perhaps one we weren't quite ready to tackle.
As of the current version, there is only the one bad ending in Sileo and it can only be triggered in Diego's route. Doing the same thing in Tai's Route for instance will result in some dialogue changes throughout the route but won't impact the actual events that take place. We received some pretty harsh feedback when that content was released and we've stuck to fairly linear route design ever since. The Polyamorous Route and Lukas' Route will be more complex and branching but won't feature bad endings in the vein of the one in question.
Writing for visual novels is certainly a learning experience. I've learned a great deal, but can and will still learn a great deal more. If you decide to give Sileo another go, hopefully our later and more recent work is more to your liking.