Interesting. I never got the impression that Roddenberry was that far "out of the loop" for the third season. And it never seemed as though Michael Piller was one to just make up stories like that out of whole cloth for the purposes of "propaganda."
I don't have Engel's book, so I can't look it up. I'll try to pick it up and find the reference.
I do have "The Continuing Mission" which is an "official" ST book, so you won't find much controversy there. However, on p. 119 (regarding the 3rd season), Piller is quoted: "Gene was beginning to go into decline. Not that he was completely uncommunicative, but it was clear that he was not the same man that he had been." I infer from that statement that Roddenberry didn't have much input at that point, or it was sporadic at best. Maybe he just didn't care about Crosby's return by that time.
And, I wouldn't say Piller made up stories. To quote Spock, "It was an exaggeration."
Anyway, I'll have to retract my statement about Roddenberry wanting to kill off Yar out of anger until I can find a reference.