I have no connection to this family but I wonder if you have confused Thomas and Timothy Murphy as on the www.irishgenealogy site the marriage of Bridget Jones of Knockdown in 1899 shows Timothy not Thomas Murphy as the groom.Also it gives Timothy's father name as Michael Murphy.
See
http://churchrecords.irishgenealogy.ie/churchrecords/details...

and this is the family of Timothy and Bridget Murphy in Derreen in the 1901 Census

http://www.census.nationalarchives.ie/pages/1901/Kerry/Derre...
and in 1911
http://www.census.nationalarchives.ie/pages/1911/Kerry/Derre...
Timothy is showing as a widower so Bridget must have died in the intervening years.
Didn't find a baptism for Timothy around 1851 but there is a later baptism that might be a possibility.

http://churchrecords.irishgenealogy.ie/churchrecords/details...
Good Luck
annclare