Since there are now takes that the tma s5 ending was more nuanced than people who dislike it give it credit for I’m just going to say: no, I don’t think Johnny meant to wholly endorse Martin & Basira & co. as uncomplicated good people making an uncomplicatedly moral choice. But. The reason people feel like the horror of it was accidental is because that’s not what the emotional beats focused on. The entire climax was written in such a way that getting a satisfying emotional response depended on being invested in the fate of jonmartin as a couple more than in anything else. If the horror had been deliberate the tone would not have been bittersweet, it would have been overwhelmingly bitter. Having I Do Not See It characters can be a well written flaw, but it doesn’t work if you make it easy for the audience to also go I Do Not See It. And the writing did allow for that - we were shown the positive (for Martin & Basira & co) consequences of the choice, that’s the note the show ended on*, and the only counterbalancing note to it was dissent from a character who was set up for a corruption arc and thus easily written off as only dissenting because he was corrupted by the Eye. I do think Johnny understood the horror of the choice M & B & co were making - but I don’t think he adequately emphasised or portrayed it, not just because of the audience response but because that audience response was shaped by what was shown and what wasn’t and what kind of emotional notes (hopeful) things ended on, and it’s the job of a horror writer to make an audience feel the full weight of horror of things that are meant to be horrifying.
*I refuse to take tmagp into consideration since that wasn’t even planned at the time