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In her absence a male employee was recruited and was "promoted over" her the woman said.
The adjudicating officer in the WRC noted that the woman did not give "lengthy consideration" to resolution suggestions.
It is not expected to precipitate a wide-scale shake up of the senior editorial team, which was overhauled in 2015.
However, Mr O'Neill is likely to name a new deputy editor, a job that will be hotly contested.
In an unusual move, Mr O'Sullivan will remain with the newspaper in a newly created role as environment, agriculture and science editor.
Mr O'Sullivan succeeded Geraldine Kennedy in 2011 as editor of 'The Irish Times'.