He should be happy. He should be fucking elated. They'd rescued Will from the Upside Down, his baby brother was alive. He was home and safe. Everything was okay now. Except for you.
No one knew exactly what you were. You looked like a person, but you didn't act like one. You didn't speak, you were animalistic and could do things similar to El. Your teeth were sharp and sometimes your eyes turned black.
Steve had tried hitting you with a bat. Eleven had tried killing you with her powers. Hell, his mother Joyce had come at you with an axe.
But then Will jumped in front. He was still so wobbly on his feet, it made Jonathan's heart clench. Will was crying and stuttering about how they "can't hurt her" and "she's his friend". Apparently, you had sniffed out Will in the Upside Down when he was first trapped. You'd been scary, and you were more monster than human. But you had protected him from the Demogorgon.
So, against Jonathan and pretty much everyone's better judgement, you were kept alive.