Haven’t you yourself said that a lot of their moves with Conner have more to do with Jon? That they sidelined Conner mainly so as not to threaten Jon’s position as Superboy and then Superman? That Matt Price may be a new Superboy because Conner still being in that role makes things awkward for Jon? None of that points to them thinking there’s a problem with Conner himself, so much as him being in the way of where they want to take Jon. Making Conner bi/gay would overshadow Jon which is precisely what you think they’re trying to avoid.