Parents are William Stewart and Hannah Elliot according to her Australian marriage certificate. I am yet to find their DOB or DOD.
In the 1891 census, Margaret is said to be "living by her own means"
It looks very much like Thomas, Margaret & William (I could not see George) travelled back to England on the ship, "Sussex" leaving Melbourne in June 1865. Their ages ties in perfectly with what we already know compared to the shipping records.
Sources
Marriage certificate
Death certificate
Parish registers sighted
Australia Marriage Index, 1788-1949
National burials index v3
1871, 1881 & 1891 English census
England & Wales, FreeBMD Death Index: 1837-1983
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DNA Connections
It may be possible to confirm family relationships with Margaret by comparing test results with other carriers of her mitochondrial DNA.
However, there are no known mtDNA test-takers in her direct maternal line.
It is likely that these autosomal DNA test-takers will share some percentage of DNA with Margaret: