I am aware that it could be either Mary.
According to a newspaper article he married Margaret Lewis nee Price at the Register Office, Cardiff.
https://newspapers.library.wales/home, Welsh Newspapers Online.
"MARRIAGE. JONES-LEWIS. —Nov. 4, at the Register Office, Cardiff, by licence, the Rev. E. E. Jones, Pencoed, to Margaret' widow of the late Thomas Lewis, Esq., Tarlan near Merthyr."
South Wales Daily News
8th November 1879 Page 2
https://newspapers.library.wales/view/3508802/3508804/6/.
I've been searching the English version of newspapers.library.wales and haven't found his 1st marriage notice.
you can't infer anything from the order of surnames for marriages on FreeBmd, it's just alphabetical. Unlikely to be a parish marriage given that he was a Baptist minister.