James Keddie and wife Isabella are NOT your Isabella's parents.
James died 1851 to 1861 - Isabella in Kingslassie 1861 and died there in 1865.
Her death is recorded on SP as Isabella Keddey - died 25/10/1865 Kingslassie, widow of James Keddey, farmer - her parents were James Gilmour and Margt., formerly Boyd i.e. Not an Isabella Scott. Their children baptised showing parents as James Keddie and Isabel Gilmer and their dau. Isabella seems to have been baptised 11/9/1821 at Kingslassie and, as ages rounded down on 1841 census, would indeed agree with her being shown as 15 on the census as she wouldn't have been 20 until later in the year.
I think your Isabella could be the Isabel Kiddie 15 who in 1841 was in Auchtertool, Fife, servant to a Kilgour family.
Isabella Brown Williamson's death certificate gives her fathers occupation as what looks like 'Procer' which perhaps should be Grocer. First letter hard to read but definitely looks like rest of word is 'rocer'. In no way looks like Farmer.
Since, although Isabella's birth/baptism doesn't appear in available records, and there also doesn't seem to be any other children born of a Keedie(Kiddie)/Scott union, I would think it more than possible that her parents were not married. Not much help to you, I know, but this has happened several times in my own Scottish ancestry. Illegitimate children frequently known by their fathers surname although parents never married. Seems to be an acceptable Scottish thing of the time.
Annette