Removing the centering option [c] to the longtable environment allows LaTeX templates to control the overall table alignment in a document by setting the longtable length variables LTleft and LTright.

Example:

\setlength\LTleft\parindent
\setlength\LTright\fill

results in left aligned tables that respect paragraph indentation.

This patch will not change the default behavior of pandoc because centering is the default for tables even if [c] is not specified.