Mary A. E. Green is found in Johnson County in 1850 as apparent widowed head of household with a number of children. I belive this is your lady as also listed in a Mary Craddock (b1775 I presume the mother of the woman in question) She is also in the PM file index in Pettis county (county seat is Sedalia) in 1864 as below:

Green, Mary; Pettis; Georgetown:
A 52 year old widow with one child, 14 year old boy; husband died in Indiana, one son died at Jefferson City in service; is destitute and requests rations.
07-30-1864 F1332

Are we sure she married a second time after 1850? Could Luther Martin Green be an illegitimate / unclaimed child of a desparate woman in war time doing desparate things thus not discussed in later years? The 14 year old listed above would be Edwin C Green. Interestingly his older sister, Irene(a) (b 1839) ends up with the Lotspeich clan of Henry County in 1870. A family well known on the board if you do a archives search. Most likely candidate for son who died in Jeff City would be Josiah Green (b 1842?).

A AG card for a Josiah Green is here and fits fairly well (He died in Cape Girardeau of all places of pneumonia) enrolling in Plattsburg MO Sept 1862 Co H 29th Infantry Volunteers.

http://www.sos.mo.gov/TIF2PDFConsumer/DispPDF.aspx?fTiff=/archives/AdjutantGeneral/Civil_War/ServiceCards/s860/1133.tif&Fln=S134400.pdf

This may be a help to you as he will have service records available that may list parent and or sibling information. Also explains why he disappears from the census rolls.

A service card for a William T Green of correct age for another of Mary A E Green son's indicate he enlisted as a substitute in St. Louis MO age 20 in 1865. Again an action of poverty. He mustered out alive in Memphis TN in 1866.

http://www.sos.mo.gov/TIF2PDFConsumer/DispPDF.aspx?fTiff=/archives/AdjutantGeneral/Civil_War/ServiceCards/s853/0109.tif&Fln=S134597.pdf

Again these last 2 are shots in the dark but maybe alleys of investigation as I know you've been looking for a long time.

John R