no conflict between someone being ‘disadvantaged’ for a choice they willingly and knowingly made, similar to choosing a Wizard or a Fighter and having to live with those consequences when it comes to character abilities
I could not care less about the DMG quote, of course it conflicts with it
Read back those two sentences you just wrote to yourself and tell me again how they don't contradict each other. Someone playing a Paladin or Cleric picks up the 5.5 PHB and DMG, and does not think they're going to be arbitrarily punished for not having the approval of their god. Then, you state that you don't care and that of course what you think conflicts with that. You have now presented a conflict yourself.
And we are discussing the current edition of the game, and why it's a good idea not to take away those class features. You can obviously do what you want at your own table, but you're clearly presenting something that is neither fair nor expected by players reading the new edition, and frankly, it's not for setting logic - it's for the novel in your head as a DM.