like dont get me wrong i enjoy a 'jonathan is gonna kill mike' joke as much as the next guy, but consider an opposing point. jonathan being the first person byler come out to, and just after, jonathan asks to pull a clearly very anxious mike aside for a second. mike thinks he's about to either a) get the shovel talk or b) skip the shovel talk, get murdered immediately, but instead. jonathan just tells him, gentle, that he's proud of him for coming out, and he's so happy that Will isn't alone in this, and that he can see how much Mike loves Will, and how happy that makes his little brother, and he is so grateful that Will has him. because mike, jonathan promises, is a good kid.
and mike -- who is so nervous about coming out, so scared of losing his parents over it and splintering his family in turn -- gets such a solid reminder that he does have a family, and does have people that want to see him happy for who he is, and he will always have somewhere to go. jonathan offering that to him.