Thanks for pointing out the episode with Jim and Alex. This at least indicates that they weren't estranged, as of 1990. I still wonder what their relationship was really like at that point, though.
Your observation about the time period when Fred became a vegetarian is astute. I'd heard about the episode with the meat pie, but I wasn't sure which one it was, or when it aired. However, I'd advise a word of caution with regard to the People article, since I know that they got at least one major fact wrong. Based on another source (the film Fred Rogers: America's Favorite Neighbor, if I recall correctly), Fred didn't leave Dartmouth for Rollins because of Joanne; they met when Fred came to Rollins. However, given independent verification that Fred was a vegetarian for many years, the People article's assertion is likely true.
I believe I'd also heard that David Newell is a vegetarian, though I don't remember the source. I want to say that it was the film Speedy Delivery, but I don't have a distinct memory of hearing that fact from the film, so it very well may have been one of the many other articles that I've read.