It would be like as if the Doctor had a rule about not littering in the TARDIS but then the floors got an upgrade so that all trash littered in the TARDIS would be transformed into environmentally friendly fuel. Would there be any point to that rule anymore?
That was damn good analogy.
Well, I think that brings up an interesting point. Maybe the rule about littering the TARDIS was never about the litter so much. The Doctor could whip out his sonic screwdriver and zap the litter in one shot. But it was a sense that he wanted his companions to respect this great machine that was not only a space/timeship, but, they're home
Now the Doctor being generally "Fantastic!" noticed that certain companions would just litter, and would actually trip or slip on litter, which would hurt them when the TARDIS is in a battle against the Dalek mothership. So being the cool Time Lord his is, he upgraded the TARDIS floors to self-clean.
Out of kindness he helped mitigate the consequence
of their littering, but that doesn't mean the rule wasn't a good one, or not valid.
Similarly, the Bible makes the point that God doesn't just come up with rules for the kicks of making people miserable. You and I don't hurt God by sinning. We hurt ourselves
. Personally, I think you're right, I don't see what's so harmful, on the surface, of a guy kissing a guy or sleeping with him. But maybe it's not just about health, or even the happiness you feel being with someone you love.
Maybe there's an even greater happiness that comes from following even God's most difficult rules. Maybe the amount of reward is directly proportional to the difficulty of the the rule.
All I'm saying is, maybe God does things for our benefit, not our misery. As always, that's my very humble opinion.