Either Lucy was just bitter over Linus perfectly tossing the letter in the mailbox, or Violet decided to let Charlie Brown come just because. Back in the early days when Linus was a baby, Charlie Brown and Violet used to play together so I don’t see her turning that far against him just because she’s on Lucy’s side.
Now that you bring it up, comparing the great pumpkin special as an allegory for Jesus makes no sense to me for a few reasons. 1. Linus is writing a list to the great pumpkin, like you do with Santa Claus not praying or anything like that. 2. Linus wanted to pick out the right pumpkin for the GP to come to, like what some kids might do when picking out a Christmas tree. 3. Linus says that if you doubt GP’s existence he won’t come to you (that’s what made some viewers believe it was about Jesus) but really thinking about it, that could be what some kids will think happen if you don’t believe in Santa. And if you rewatch the episode, it’s obvious the great pumpkin is just a Halloween version of Santa. I just wish it had ended with Linus finally accepting that the Great Pumpkin didn’t exist after all, but coming to understand that doesn’t ruin his favorite holiday. On the bright side, Charlie Brown came out lucky in this… sort of. Hey, those rocks can make good slingshot weapons.