Jay Leno treated Conan O'Brien fairly when it came to leaving his job and allowing him to come in a fill his place. It probably was hard after all those years working on the set and then having to turn your job you went to everyday over to someone else.
Yes Jay Leno did he left just to come back and take his old job back. He caused a lot of problems he didn't help the night time talk show scene. Everyone is sick of Jay Leno he just might do this again this time with Jimmy Fallon taking his spot.
Jay Leno and Conan O'Brien are professionals. In the entertainment industry no less. When your ratings drop then you aren't as valuable a commodity as someone else is. Was Conan hurt by the Tonight Show? Yes, but they were not treating him unfairly. There isn't a sense of putting in your time in Hollywood.
I believe that any time in television the producers and network executives have more power then anyone else over whose show replaces who, I don't think Jay Leno had any influence in the Conan O'Brien show being cancelled and I believe both men probably have a good and friendly relationship.