I’d say the practices you see at First Springfield fall somewhere between Baptist and Methodist.
She’s been shown with her Bodhi tree a few times since then. There’s no reason to think she’s changed her mind at all. I think the family may have been seen at church since that episode, but Lisa realizes (thanks to Gere) that she can go to church and celibrate Christian holidays with her family if it makes her and them happy, and still be true blue Buddhist. Or yellow. But anyway, she’s still one.
Since when is Scientology trendy? It gets ridiculed all the time, and I think the Simpsons have lent a hand to that.