While I agree it is unfortunate Faye Marsay didn't get to be a companion, given the trajectory of her career since, I'd say things worked out just fine for her.
RTD did express a similar concern in The Writer's Tale when talking about it was announced Catherine Tate was returning to be the full time companion in the fourth season, that because of the timing everyone would think Freema Agyeman was fired despite the fact that the ending to S3 was written well in advance of deciding to bring Donna back.
An alternate ending was filmed for Parting of the Ways with Eccleston staying in the role which would have instead been a cliffhanger setting up Rose's storyline for the second season. Though it's been debated over the years as to whether this was in fact an alternate plan for Eccleston staying or if it was just intended to be used in the press screenings for the episode in order to keep the regeneration secret for the actual broadcast of the episode.
I don't know about that. Given death and mortality are such a central theme to Capaldi's second season, I get the impression that likely would have been the case regardless if Clara or Shona were the companion. With that in mind, I suspect the final three episode arc might well be the same anyway.
