Rick Berman states his is interview with the Archive of American Television that McFadden and first/second season executive producer Maurice Hurley could not stand one another, and that he wanted her gone. Hurley is also the person that has been mentioned as having been involved in the sexual harassment allegations. In any event, Hurley got his way, and she was let go.
At the end of season two, it was decided that Pulaski wasn't working out. By this time, Hurley was on his way out the door, and it was up to Berman to decide whether to cast a third doctor or bring back Crusher. He lobbied for Crusher's return, Roddenberry gave his blessing, and she came back.