Mrs McAlpine, only recently selected for the pound;80,000 a year post to succeed Ian McMurdo, had became embroiled in a row over her husband's criminal past.
While she was head of Viewforth High in Kirkcaldy in 1998, her husband was jailed for 10 years for sexual offences against a girl.
It is believed West Dunbartonshire was not aware of the association before she accepted the post but later maintained it was "fully supporting" her appointment.
Mrs McAlpine, who has been separated from her husband for some time, moved on to become a headteacher in Newcastle upon Tyne and hit the headlines when she featured in a Channel 4 programme on "superheads".
She has recently been director of the education action zone in Great Yarmouth.
Bob Cook takes over as acting director for several months before he, too, moves on to the TAC team at the Convention of Scottish Local Authorities which is guiding the post-McCrone programme.
Previous applicants for the post will be reconsidered.