Wasn't Roddenberry still in charge during the third season? Anyway, I guess he brought Muldaur in, knowing her from TOS.
This is what MA (http://memory-alpha.org/en/wiki/Gates_McFadden
) has to offer about the subject, but they give no source for their information:
McFadden left the series during the second season, replaced by Diana Muldaur as Doctor Katherine Pulaski. Officially, the producers felt that the character of Crusher had not developed as well as they had hoped. Unofficially, there were some disagreements between the show's producers and McFadden as to how the character should develop, which may have led to some bad blood between her and several executive producers, resulting in McFadden's being released from her contract before the second season. But thanks to a letter-writing campaign, support from Patrick Stewart, and a personal invitation from Rick Berman, McFadden was brought back to the TNG cast for the third and subsequent seasons.