Honestly, the only thing I think he is to blame is not trusting Stan or Mabel about the Rift. I thought it was sweet he wanted Dipper as an apprentice. And that before the whole Aliens Sphere thing.

Ford probably shouldn't have kept the rift secret from the rest of the family, but aside from that he did nothing wrong, as far as I'm concerned. If anyone was in the wrong in this episode, it was Mabel. For Dipper, staying in Gravity Falls with Ford is a too fantastic opportunity to turn it down, and if she wants to be with her brother, why not ask to let her stay with them in Gravity Falls as well? Surely that would be the outcome that everyone would be happy with.