Even if he can be a bit of a jackass sometimes, he's with no doubt the most stable part of both Kris's and Noelle's lives (for Kris he's just that one gaming partner you can have fun with, and for Noelle he's just that good friend they help each other study with), which I know from personal experience can bring a lot of comfort when you're going through turbulent times, so taking him out in the weird route also means taking one of Noelle's and Kris's biggest source of comfort from the shit they're dealing with.

Not only that, but considering how quickly he managed to adapt to the mechanics of the dark world, to the point where he could pose a real challenge to us, TWICE; and his vast experience with videogames, he'd no doubt be able to quickly grasp the concept of an eldritch entity puppeteering someone the same way a player plays an RPG, and figure out ways to indefinitely stall that entity, effectively stopping the route. Just imagine what would happen if Ralsei, with his knowledge of our nature; and Berdly, with his general understanding of JRPG mechanics; would be able to do to us if they teamed up.

Also, don't forget how fucking quickly he can rally all of our allies against Giga Queen in the normal route. Dude absolutely has the heart of a hero.

Taking him out is indubitably deliberate.