Whereas in the webtoon, Hyun Soo started liking her for the shallow reason that she looked like Maria.

It's just him being a teenager and seeing and being near a pretty girl. He was listening in on the trainee girl next door changing clothes and was getting flustered and blushed when Eun ran up to hug him.

He started actually liking her because of the way she treated him: treating him like family and having his back, which he so desperately needed. She was pretty much acting like a big sister when they had that talk. Besides, the story also insinuates how she resembles Maria in personality and character as well.

So by doing so, I felt like the author just threw away Hyun Soo's real desire and how his monster side came to be

You answered this yourself. He became a monster to protect his new family. The story even builds this up from his first encounter with the kids to Jayhun's death nearly breaking him to seeing Jisu get hurt. Of course, Jisu is the most important person to him and the one he wanted to save most, but it wasn't just because of her.

He wanted to save everyone, but that was impossible due to the nature of being a monster. So he had to compromise. Instead of just saving everyone, it became kill the monsters in his way to save everyone much like how Hyuk's desire was purely to stop Hyun and nothing else. Saving everyone is just collateral. And Hyun still ended up attacking them once he fully gave in, anyway.