The only reason he burned his relatives is because they betrayed him not because they were hertics (in the show he did that but in the book it was explained that his brother in law was trying to sell him out). If the red God chooses someone else how is that a betrayal? He does not even worship the Gods but are using them to further his own goals.
and you could agree that Mel choosing Jon would be betrayal right? Remember, he's fukking Mel too. You think with Stannis' twisted sense of justice, he's just gonna take being called "The warrior of light" and "Azor Ahai" and all that other stuff, for Mel to flip and say "oh my bad its really this kid who's the b*stard son of your older brother" (as far as he knows).
You think Stannis is gonna be ok with that. After you know how salty he was about Robert liking Renly more?