Yes, ToDoOrNotToDo meant Peggy did an eye flicker at Trudie, not Betty.
Peggy is bothered about Pete IMO - that was why she asked Don who was going to the new company and when Don wouldn't tell her, she was about to refuse to come, but then Don cried at her and she caved (let's face it, who wouldn't).
I don't think Peggy wants to be with Pete - but she doesn't want to work with him. Understandably. Must make things a bit awkward round the coffee machine if you've had your colleague's illegitimate baby and hushed the whole thing up.
My favourite bit of the last show was when Roger Sterling told Peggy to make him coffee and she just said "no" without even looking up