The Thomas Nixon who married Agnes Meek had a father named Thomas Nixon (not Joseph), according to the 1892 marriage certificate:
https://civilrecords.irishgenealogy.ie/churchrecords/images/marriage_re…
The birth you found in Galgorm in 1869 looks to be for a different Thomas Dixon. Have you found your Thomas’s death certificate in Scotland? If so, it should list both his parents names.
This looks to be Agnes parents in 1901:
http://www.census.nationalarchives.ie/pages/1901/Antrim/Ahoghill/Lisnaf…
The Moravians kept excellent birth, death and marriage records so you may be able to trace her family back to the 1700s. There’s a copy of the records in PRONI in Belfast.