I think the only reason Belle isn’t getting the villain treatment is because this is Rumple’s HEA– so no way would he turn her into a villain while he’s a hero. In his HEA, they are married and in love. So, everything changes, except for Belle and that’s because the Author is writing the story for himself.
It just occurred to me that seeing this HEA in the AU could be more evidence that Rumple will die once everything is set right again. If Rumbelle won’t be living HEA as the show continues, showing them happy and together in the AU is the writers throwing the shippers a consolation prize.
They’ve just had Regina realise she shouldn’t use Isaac to change her story, but Rumple is persisting, and it’d be quite the cruel lesson for him to learn if he gets a temporary taste of what could have been, before having to pay the ultimate price for the magic he used to try and get that HEA.