Was it a tad bit out of character for Mary, Lou, and Murray in the "Ted's Moment of Glory" (https://www.imdb.com/title/tt0642897/) episode (from Season 6) to suddenly not want Ted to go? Did they ever before, show any real affection or like for Ted? It seemed like they only tolerated him and Lou was happy to be shed of him for any reason on prior occasions.

It sure was. It seems like they were just determined to praise themselves as fake news people.

Ted's whole existence at WJM was a mystery. Was it just a crap station like WKRP, but without the sense that they were trying to get better?

Right! They had their chance to get rid of him, and Ted had the chance at big money doing something fun.
After the finale, when the ratings for WJM didn't improve, I figure Ted got fired too, and then went to Hollywood to become a game show host.