OK so hear me out.
Maybe the reason Jim Hopper actually thought it was NOT NORMAL OR HEALTHY for Mike and El to be together was because he was there when Mike and Will were being vulnerable in the shed. He knows about Will's drawing of a Rainbow Ship. He heard Mike say "You said yes, you said yes. It was the best thing I've ever done." with tears in his eyes and how they looked at each other.
Hopper knows what's up.
He's trying to protect is daughter from getting her heart broken from a closeted gay boy.